%matplotlib inline
import pandas as pd
import numpy as np
import re
import os
import math
from multiprocessing import Pool
from tqdm import tqdm
from scipy import stats
## init
mySpecie='Homo_sapiens'
#prealigned_dir='/cellar/users/btsui/all_seq_snp/Homo_sapiens_all_merged_snp.TCGA.prealigned.pickle'
targetted_align_dir='/cellar/users/btsui/all_seq_snp/Homo_sapiens_all_merged_snp.TCGA.pickle'
manifest_dir='/cellar/users/btsui/Project/METAMAP/notebook/RapMapTest/XGS_WGS/./tcga_lgg_wgs_bams.df.wxs_rnaseq.pickle'
targetted_df=pd.read_pickle(targetted_align_dir).loc["TCGA"]
all_UUIDs=targetted_df.index.get_level_values('Run_digits').unique()
#883, 1427
print ('n UUID:',len(all_UUIDs))
n UUID: 1570
manifest_df=pd.read_pickle(manifest_dir)
manifest_df['processed']=manifest_df.file_id.isin(all_UUIDs)
uuid_barcode_mapDf=pd.read_csv('/cellar/users/andreabc/GDC_barcodes/uuid_barcode_map.txt',sep='\t').set_index('file_id')
manifest_df['sample_barcode']=uuid_barcode_mapDf.loc[manifest_df.file_id]['sample_barcode'].values
m_data_category=manifest_df.data_category=='Raw Sequencing Data'
m_experimental_strategy=manifest_df['experimental_strategy'].isin(['RNA-Seq','WXS'])
manifest_df_sub=manifest_df[manifest_df['processed']&m_data_category&m_experimental_strategy]
tmpVC=manifest_df_sub['sample_barcode'].value_counts()
#identify data with both RNAseq and WXS
with_both=tmpVC.index[tmpVC==2]
manifest_df_w_RNA_WXS=manifest_df_sub[manifest_df_sub.sample_barcode.isin(with_both)]
inVcfDir='/data/cellardata/users/btsui/dbsnp/Homo_sapiens/All_20170710.f1_byte2_not_00.vcf.gz'
vcfDf=pd.read_csv(inVcfDir,sep='\t',header=None)
vcfDf.columns=['Chr','Pos','RsId','RefBase','AltBase','','','Annot']
vcfDf['Chr']=vcfDf['Chr'].astype(np.str)
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py:2785: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False. interactivity=interactivity, compiler=compiler, result=result)
refI=vcfDf.drop_duplicates(['Chr','Pos','RefBase']).set_index(['Chr','Pos','RefBase']).index
"""for _,vcfDfRowS in vcfDf.iterrows():
query_chromosome,qeury_corrdinate=vcfDfRowS['Chr'],vcfDfRowS['Pos']
selectedBase=vcfDfRowS['AltBase']
break"""
#varscanVcfMerged=pd.read_pickle('/cellar/users/btsui/Project/METAMAP/notebook/RapMapTest/XGS_WGS/Data/TCGA_VCF.varscan_dr.pickle')
vcfDf[vcfDf.Pos==142877758 ]
Chr | Pos | RsId | RefBase | AltBase | Annot | |||
---|---|---|---|---|---|---|---|---|
184405 | 8 | 142877758 | rs75717953 | T | C | . | . | RS=75717953;RSPOS=142877758;dbSNPBuildID=131;S... |
#topTcgaVcfDf=varscanVcfMerged['one_vcf_df'].groupby(
# ['CHROM','POS','ALT']).size().sort_values(ascending=False).reset_index(name='Count')#.iloc[:100]
#topTcgaVcfDf.iloc[:100]
#371/524.0
#topTcgaVcfDf['Count']
#topTcgaVcfDf['CHROM']=topTcgaVcfDf['CHROM'].str.replace('chr','')
#tmpDf=topTcgaVcfDf.set_index(['CHROM','POS'],drop=False)
#targetted_multI=vcfDf.set_index(['Chr','Pos']).index
#%time existingVC=targetted_df.groupby(['Chr','Pos']).size()
#topTcgaVcfDf_inTargeted=tmpDf[tmpDf.index.isin(targetted_multI)]
manifest_df_w_RNA_WXS.head()
access | annotations | cases | data_category | data_format | data_type | experimental_strategy | file_id | file_name | file_size | platform | processed | sample_barcode | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
546 | controlled | NaN | [{'project': {'project_id': 'TCGA-LGG'}, 'case... | Raw Sequencing Data | BAM | Aligned Reads | RNA-Seq | 1985b367-00c4-4c25-b049-5858e937cc6d | 948a7b5a-de83-41db-85f1-93a1a9b109ba_gdc_realn... | 3293981085 | Illumina | True | TCGA-HT-A4DV-01A |
1019 | controlled | NaN | [{'project': {'project_id': 'TCGA-LGG'}, 'case... | Raw Sequencing Data | BAM | Aligned Reads | RNA-Seq | a7aff6a7-cea4-42e9-8d56-b211843a0302 | 8e4c32f5-1ed2-453b-b029-db7836249d3b_gdc_realn... | 4070637137 | Illumina | True | TCGA-HT-A4DS-01A |
860 | controlled | NaN | [{'project': {'project_id': 'TCGA-LGG'}, 'case... | Raw Sequencing Data | BAM | Aligned Reads | RNA-Seq | 4038984b-21d1-45d3-a5bb-208f9e71aa78 | b52aeb27-8d06-4a1c-b322-ee947261e95c_gdc_realn... | 4195199173 | Illumina | True | TCGA-FG-A4MW-01A |
791 | controlled | NaN | [{'project': {'project_id': 'TCGA-LGG'}, 'case... | Raw Sequencing Data | BAM | Aligned Reads | RNA-Seq | 7b17a5ef-c778-4753-8c30-427af9171f7a | a9bfcb6f-ce2b-47e2-a2e2-dd777b6d1344_gdc_realn... | 4436516715 | Illumina | True | TCGA-DB-A4XC-01A |
1285 | controlled | NaN | [{'project': {'project_id': 'TCGA-LGG'}, 'case... | Raw Sequencing Data | BAM | Aligned Reads | RNA-Seq | 93e20db7-4892-4ef8-9331-ecd665e4cb91 | 33262d51-82cb-4fe6-89d1-b7e1c4673896_gdc_realn... | 4501820893 | Illumina | True | TCGA-FG-A4MX-01A |
Index(['TCGA-P5-A5EV-01A', 'TCGA-TQ-A7RI-01A', 'TCGA-HT-7478-01A', 'TCGA-QH-A6X8-01A', 'TCGA-HT-7472-01A', 'TCGA-HW-7495-01A', 'TCGA-DU-7007-01A', 'TCGA-QH-A6CU-01A', 'TCGA-DB-A64R-01A', 'TCGA-DU-A6S2-01A', ... 'TCGA-QH-A65Z-01A', 'TCGA-RY-A845-01A', 'TCGA-S9-A6U9-01A', 'TCGA-DH-A7UV-01A', 'TCGA-DU-6402-01A', 'TCGA-DU-6404-01A', 'TCGA-WH-A86K-01A', 'TCGA-DU-A5TP-01A', 'TCGA-HT-A61B-01A', 'TCGA-HT-7677-01A'], dtype='object', length=524)
querySample='TCGA-HT-A4DV-01A'
statDict={}
for querySample in tqdm(with_both):
manifest_dmanifest_g=manifest_df_w_RNA_WXS.groupby(['sample_barcode','experimental_strategy'])#['file_id']
rnaseqUUID=manifest_dmanifest_g.get_group((querySample,'RNA-Seq'))['file_id'].iloc[0]
wxsUUID=manifest_dmanifest_g.get_group((querySample,'WXS'))['file_id'].iloc[0]
wxsTargettedDf=targetted_df.loc[wxsUUID].reset_index().set_index(['Chr','Pos'])
wxsChrPosCountS=wxsTargettedDf.groupby(['Chr','Pos']).size()
### take only sites with one allele detected
homozygous_pos=wxsChrPosCountS[wxsChrPosCountS==1].index
m_homozygous=wxsTargettedDf.index.isin(homozygous_pos)
wxsTargettedDf_homo=wxsTargettedDf[m_homozygous]
wxsTargettedDf_homo=wxsTargettedDf_homo.reset_index().set_index(['Chr','Pos','base'])
wxsTargettedDf_homo['is_ref_base']=wxsTargettedDf_homo.index.isin(refI)
(~wxsTargettedDf_homo['is_ref_base']).mean()
### ignore the references
homoGermlineVariantDf=wxsTargettedDf_homo[(~wxsTargettedDf_homo['is_ref_base'])&(wxsTargettedDf_homo['ReadDepth']>=2)&(wxsTargettedDf_homo['AverageBaseQuality']>=30)]
## check against RNAseq for the variants
#For homozygous germ line variants, only the reference allele are supposed to be detected
rnaTagettedDf=targetted_df.loc[rnaseqUUID]
rnaTagettedDf=rnaTagettedDf[rnaTagettedDf['AverageBaseQuality']>=30]
rnaseqSiteI=rnaTagettedDf.reset_index().set_index(['Chr','Pos']).index
wxsHomoSiteI=homoGermlineVariantDf.reset_index().set_index(['Chr','Pos']).index
interRd=np.intersect1d(wxsHomoSiteI[homoGermlineVariantDf['ReadDepth']>=10],rnaseqSiteI[rnaTagettedDf['ReadDepth']>=10])
nsitesWithReads=len(interRd)
#print (nsitesWithReads)
homoGermlineVariantDf.head()
tmpDf=rnaTagettedDf.unstack()['ReadDepth']
rnaTagettedFractS=(tmpDf.T/tmpDf.sum(axis=1)).T.stack().to_frame('AllelicFract')
#inter
wgxGermlineVarM=rnaTagettedFractS.reset_index().set_index(['Chr','Pos','base']).index.isin(homoGermlineVariantDf.index)
germLineDf=rnaTagettedFractS[wgxGermlineVarM]
statDict[querySample]={'percentage_germline_var_with_1_AF':(germLineDf['AllelicFract']==1.0).mean(),
'nsites_overlap':nsitesWithReads,
'is_alt':(~wxsTargettedDf_homo['is_ref_base']).mean()}
23%|██▎ | 119/524 [10:04<34:18, 5.08s/it]
--------------------------------------------------------------------------- KeyboardInterrupt Traceback (most recent call last) <ipython-input-21-adfef1900d68> in <module>() 12 ### take only sites with one allele detected 13 homozygous_pos=wxsChrPosCountS[wxsChrPosCountS==1].index ---> 14 m_homozygous=wxsTargettedDf.index.isin(homozygous_pos) 15 wxsTargettedDf_homo=wxsTargettedDf[m_homozygous] 16 wxsTargettedDf_homo=wxsTargettedDf_homo.reset_index().set_index(['Chr','Pos','base']) ~/anaconda3/lib/python3.6/site-packages/pandas/core/indexes/multi.py in isin(self, values, level) 2936 if level is None: 2937 values = MultiIndex.from_tuples(values, -> 2938 names=self.names).values 2939 return algos.isin(self.values, values) 2940 else: ~/anaconda3/lib/python3.6/site-packages/pandas/core/indexes/multi.py in from_tuples(cls, tuples, sortorder, names) 1354 arrays = lzip(*tuples) 1355 -> 1356 return MultiIndex.from_arrays(arrays, sortorder=sortorder, names=names) 1357 1358 @classmethod ~/anaconda3/lib/python3.6/site-packages/pandas/core/indexes/multi.py in from_arrays(cls, arrays, sortorder, names) 1298 from pandas.core.arrays.categorical import _factorize_from_iterables 1299 -> 1300 labels, levels = _factorize_from_iterables(arrays) 1301 if names is None: 1302 names = [getattr(arr, "name", None) for arr in arrays] ~/anaconda3/lib/python3.6/site-packages/pandas/core/arrays/categorical.py in _factorize_from_iterables(iterables) 2541 # For consistency, it should return a list of 2 lists. 2542 return [[], []] -> 2543 return map(list, lzip(*[_factorize_from_iterable(it) for it in iterables])) ~/anaconda3/lib/python3.6/site-packages/pandas/core/arrays/categorical.py in <listcomp>(.0) 2541 # For consistency, it should return a list of 2 lists. 2542 return [[], []] -> 2543 return map(list, lzip(*[_factorize_from_iterable(it) for it in iterables])) ~/anaconda3/lib/python3.6/site-packages/pandas/core/arrays/categorical.py in _factorize_from_iterable(values) 2513 codes = values.codes 2514 else: -> 2515 cat = Categorical(values, ordered=True) 2516 categories = cat.categories 2517 codes = cat.codes ~/anaconda3/lib/python3.6/site-packages/pandas/core/arrays/categorical.py in __init__(self, values, categories, ordered, dtype, fastpath) 343 if dtype.categories is None: 344 try: --> 345 codes, categories = factorize(values, sort=True) 346 except TypeError: 347 codes, categories = factorize(values, sort=False) ~/anaconda3/lib/python3.6/site-packages/pandas/util/_decorators.py in wrapper(*args, **kwargs) 175 else: 176 kwargs[new_arg_name] = new_arg_value --> 177 return func(*args, **kwargs) 178 return wrapper 179 return _deprecate_kwarg ~/anaconda3/lib/python3.6/site-packages/pandas/core/algorithms.py in factorize(values, sort, order, na_sentinel, size_hint) 633 from pandas.core.sorting import safe_sort 634 try: --> 635 order = uniques.argsort() 636 order2 = order.argsort() 637 labels = take_1d(order2, labels, fill_value=na_sentinel) KeyboardInterrupt:
statDf=pd.DataFrame(statDict).T
import seaborn as sns
sns.boxplot(data=statDf)
<matplotlib.axes._subplots.AxesSubplot at 0x2ac218c55c50>
ax=statDf['percentage_germline_var_with_1_AF'].hist(normed=True)
ax.grid(False)
ax.set_xlabel('percentage_germline_var_with_1_AF')
ax.set_ylabel('% of RNAseq samples')
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/matplotlib/axes/_axes.py:6462: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg. warnings.warn("The 'normed' kwarg is deprecated, and has been "
Text(0,0.5,'% of RNAseq samples')
statDf.quantile(axis=0,q=0.025)
is_alt 0.106553 nsites_overlap 3515.250000 percentage_germline_var_with_1_AF 0.955057 Name: 0.025, dtype: float64
statDf.median(axis=0)
is_alt 0.112343 nsites_overlap 5827.000000 percentage_germline_var_with_1_AF 0.971341 dtype: float64
(germLineDf['AllelicFract']==1.0).mean()
0.987914744012305
rnaTargettedReI=rnaTagettedDf[rnaseqSiteI.isin(interRd)].reset_index().set_index(['Chr','Pos','base'])#[interRd]#
rnaTargettedReI['in_homo']=rnaTargettedReI.index.isin(homoGermlineVariantDf.index)
rnaTargettedReI.in_homo.mean()
0.9769743920809124
rnaTargettedReI
ReadDepth | in_homo | |||
---|---|---|---|---|
Chr | Pos | base | ||
1 | 1013541 | C | 1.000000 | True |
1046551 | G | 1.000000 | True | |
1049927 | G | 1.000000 | True | |
1338000 | C | 1.000000 | True | |
1338032 | G | 1.000000 | True | |
1338044 | G | 1.000000 | True | |
1338086 | A | 1.000000 | True | |
1338092 | A | 1.000000 | True | |
1338096 | C | 1.000000 | True | |
1338098 | G | 1.000000 | True | |
1338107 | C | 1.000000 | True | |
1398672 | C | 1.000000 | True | |
2306122 | G | 1.000000 | True | |
2406580 | C | 1.000000 | True | |
2408713 | C | 1.000000 | True | |
2408714 | A | 1.000000 | True | |
2408760 | G | 1.000000 | True | |
10375266 | A | 1.000000 | True | |
11792316 | A | 1.000000 | True | |
11796340 | C | 1.000000 | True | |
11846007 | C | 1.000000 | True | |
11950377 | C | 1.000000 | True | |
11950455 | C | 1.000000 | True | |
11998841 | T | 1.000000 | True | |
12022869 | G | 1.000000 | True | |
15933236 | C | 1.000000 | True | |
16986614 | A | 1.000000 | True | |
16986848 | A | 1.000000 | True | |
16986885 | G | 1.000000 | True | |
16987159 | C | 0.014388 | False | |
... | ... | ... | ... | ... |
X | 154357466 | G | 1.000000 | True |
154358335 | A | 1.000000 | True | |
154359271 | G | 1.000000 | True | |
154359619 | T | 1.000000 | True | |
154359789 | A | 1.000000 | True | |
154360265 | T | 1.000000 | True | |
154364108 | T | 1.000000 | True | |
154379719 | A | 1.000000 | True | |
154380001 | T | 1.000000 | True | |
154380246 | A | 1.000000 | True | |
154380976 | T | 1.000000 | True | |
154414148 | A | 1.000000 | True | |
154420665 | C | 1.000000 | True | |
154420704 | C | 0.017241 | False | |
T | 0.982759 | True | ||
154442419 | C | 0.002853 | False | |
T | 0.997147 | True | ||
154532439 | G | 1.000000 | True | |
154533012 | C | 1.000000 | True | |
154546045 | C | 1.000000 | True | |
154556194 | C | 0.983051 | True | |
T | 0.016949 | False | ||
154556237 | G | 1.000000 | True | |
154560549 | T | 1.000000 | True | |
154765467 | T | 1.000000 | True | |
154765524 | G | 1.000000 | True | |
154765948 | T | 1.000000 | True | |
155090807 | C | 1.000000 | True | |
155260815 | T | 1.000000 | True | |
155506930 | G | 1.000000 | True |
4647 rows × 2 columns
rnaReadDepthDf=rnaTagettedDf.unstack()['ReadDepth'].fillna(0)
rnaReadDepthFracDf=(rnaReadDepthDf.T/rnaReadDepthDf.sum(axis=1)).T
rnaSeqS=rnaReadDepthFracDf.stack()
#rnaReadDepthDf.head()
#rnaTagettedDf
"""
the germline variants are recoved in
58% of the homoGermline varianst can be recoved in RNAseq
"""
features | ReadDepth | AverageBaseQuality | is_ref_base | ||
---|---|---|---|---|---|
Chr | Pos | base | |||
1 | 1013541 | C | 34 | 30 | False |
1041950 | C | 38 | 29 | False | |
1042190 | A | 18 | 31 | False | |
1043223 | C | 10 | 31 | False | |
1045707 | G | 43 | 27 | False | |
1046551 | G | 33 | 28 | False | |
1047561 | C | 62 | 31 | False | |
1049927 | G | 54 | 31 | False | |
1051820 | T | 28 | 32 | False | |
1086035 | G | 27 | 31 | False | |
1232684 | G | 29 | 32 | False | |
1338000 | C | 26 | 32 | False | |
1338032 | G | 29 | 31 | False | |
1338044 | G | 31 | 31 | False | |
1338086 | A | 18 | 29 | False | |
1338092 | A | 16 | 31 | False | |
1338096 | C | 16 | 30 | False | |
1338098 | G | 17 | 30 | False | |
1338107 | C | 16 | 25 | False | |
1398672 | C | 57 | 32 | False | |
1955672 | G | 67 | 32 | False | |
2024923 | A | 33 | 33 | False | |
2229045 | G | 23 | 27 | False | |
2306122 | G | 14 | 32 | False | |
2406580 | C | 44 | 32 | False | |
2408713 | C | 19 | 32 | False | |
2408714 | A | 21 | 32 | False | |
2408760 | G | 46 | 34 | False | |
3402939 | T | 73 | 29 | False | |
3403006 | G | 25 | 31 | False | |
... | ... | ... | ... | ... | ... |
X | 154966119 | T | 60 | 31 | False |
154966498 | G | 37 | 34 | False | |
154966616 | C | 60 | 33 | False | |
154966617 | T | 58 | 33 | False | |
154969396 | G | 82 | 34 | False | |
154969432 | G | 116 | 29 | False | |
154984784 | T | 89 | 31 | False | |
154996995 | T | 143 | 31 | False | |
154999531 | T | 98 | 31 | False | |
154999543 | C | 107 | 33 | False | |
155090807 | C | 13 | 32 | False | |
155260815 | T | 141 | 31 | False | |
155506930 | G | 75 | 34 | False | |
Y | 5057021 | G | 48 | 33 | False |
5207530 | G | 44 | 33 | False | |
5207641 | C | 104 | 32 | False | |
5207717 | C | 45 | 32 | False | |
10175852 | C | 20 | 31 | False | |
16618833 | C | 57 | 29 | False | |
16618838 | C | 56 | 34 | False | |
26329144 | A | 19 | 31 | False | |
26332935 | C | 118 | 32 | False | |
26333008 | A | 53 | 31 | False | |
26333079 | G | 20 | 33 | False | |
26333764 | G | 34 | 34 | False | |
26337383 | A | 34 | 31 | False | |
26401079 | A | 12 | 32 | False | |
26420452 | C | 25 | 33 | False | |
26420477 | G | 29 | 27 | False | |
26557077 | T | 88 | 33 | False |
15630 rows × 3 columns
#rnaseqSiteI.isin(wxsHomoSiteI).mean()
0.06863206314358894
interI=np.intersect1d(homoGermlineVariantDf.index ,(rnaSeqS.index))
homoGermlineVariantDf.index.isin(interI).mean()
0.5880358285348688
rnaSeqS
Chr Pos base 1 1013541 C 1.000000 1042190 A 1.000000 1046551 G 1.000000 1049927 G 0.988764 1051820 T 1.000000 1338000 C 1.000000 1338032 G 1.000000 1338044 G 1.000000 1338086 A 1.000000 1338092 A 1.000000 1338096 C 1.000000 1338098 G 1.000000 1338107 C 1.000000 1398672 C 1.000000 2229045 G 1.000000 2306122 G 1.000000 2406580 C 1.000000 2408713 C 1.000000 2408714 A 1.000000 2408760 G 1.000000 3411655 C 1.000000 3478076 G 1.000000 3478110 C 1.000000 5877256 C 1.000000 5877331 T 1.000000 7640514 T 1.000000 7663384 C 1.000000 7663428 C 1.000000 7809988 C 1.000000 7827433 C 1.000000 ... X 154420878 G 1.000000 154442419 T 0.995726 154532439 G 1.000000 154533012 C 1.000000 154546045 C 1.000000 154556194 C 0.983051 154556237 G 1.000000 154560549 T 1.000000 154563953 T 1.000000 154765467 T 1.000000 154765524 G 1.000000 154765948 T 1.000000 154776813 C 1.000000 154837734 C 1.000000 154860536 C 1.000000 154861741 T 1.000000 154863191 G 1.000000 154896092 G 1.000000 154929458 A 1.000000 154929489 T 1.000000 154930240 C 1.000000 155090807 C 1.000000 155260815 T 1.000000 155506930 G 1.000000 Y 5207641 C 1.000000 16618833 C 1.000000 16618838 C 1.000000 26332935 C 1.000000 26420452 C 1.000000 26420477 G 1.000000 Length: 9191, dtype: float64
m=rnaSeqS.index.isin(homoGermlineVariantDf.index)
allelicFractionInGermlineS=rnaSeqS[m]
m.mean()
0.017158015785897235
len(allelicFractionInGermlineS)
9191
len(allelicFractionInGermlineS)
9191
#allelicFractionInGermlineS[allelicFractionInGermlineS==0]
ax=allelicFractionInGermlineS[allelicFractionInGermlineS>=0].hist(bins=10,normed=True)
ax.set_xlabel('Allelic fraction')
ax.set_ylabel('% of germline variants')
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/matplotlib/axes/_axes.py:6462: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg. warnings.warn("The 'normed' kwarg is deprecated, and has been "
Text(0,0.5,'% of germline variants')
rnaSeqS[rnaSeqS.index.isin(homoGermlineVariantDf.index)].hist()
<matplotlib.axes._subplots.AxesSubplot at 0x2b654652b358>
germlineVariantDf.index.isin(rnaTagettedDf.index).mean()
0.5867562380038388
#topTcgaVcfDf_inTargeted.head()
threshold=2
#### extract all the germ line variants,
#threshold=2
#selectedBase='T'
#query_chromosome, qeury_corrdinate='2',208248388
failedS_L=[]
roc_auc_l=[]
m_chr=targetted_df.index.get_level_values('Chr')==query_chromosome
Pos_array=targetted_df.index.get_level_values('Pos')
successCount=0
for vcfIndex,vcfDfRowS in topTcgaVcfDf_inTargeted.iterrows():
try:
query_chromosome,qeury_corrdinate=vcfDfRowS['CHROM'].replace('chr',''),vcfDfRowS['POS']
selectedBase=vcfDfRowS['ALT']
window_size=0
m_pos=(Pos_array>=(qeury_corrdinate-window_size))&(Pos_array<=(qeury_corrdinate+window_size))
if m_pos.sum()<10:
print ('failed')
continue
m_qual=targetted_df['AverageBaseQuality']>=30
#if m_pos.sum()>=0:
targetted_df_sub=targetted_df[m_pos&m_qual]
index_metaDf=targetted_df_sub.index.to_frame()
index_metaDf['sample_barcode']=manifest_df_w_RNA_WXS.set_index('file_id').loc[index_metaDf['Run_digits']]['sample_barcode'].values
multI=index_metaDf.set_index(['sample_barcode','Run_digits','Chr','Pos','base']).index
targetted_df_sub.index=multI
rnaseq_uuids=manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS['experimental_strategy']=='RNA-Seq']['file_id'].unique()
m_uuid=targetted_df_sub.index.get_level_values('Run_digits').isin(rnaseq_uuids)
rnaseq_df=targetted_df_sub[m_uuid]
groupings_L=['sample_barcode','Chr','Pos','base']
rnaseq_df=rnaseq_df.groupby(groupings_L).first()
wxs_uuids=manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS['experimental_strategy']=='WXS']['file_id'].unique()
m_uuid=targetted_df_sub.index.get_level_values('Run_digits').isin(wxs_uuids)
wxs_df=targetted_df_sub[m_uuid]
wxs_df=wxs_df.groupby(groupings_L).first()
mergedDf=pd.concat([ rnaseq_df,wxs_df],axis=1,keys=['rna-seq','wxs'])
mergedDf['wxs']['ReadDepth']=mergedDf['wxs']['ReadDepth'].fillna(0)
#mergedDf
#for the whole
from sklearn import metrics
#### get the homozygous
wxsWithDataDf=mergedDf#[mergedDf['wxs']['ReadDepth']>=threshold]
sampleRdS=wxsWithDataDf['wxs'].groupby('sample_barcode')['ReadDepth'].sum()
sampleRdS_rnaseq=wxsWithDataDf['rna-seq'].groupby('sample_barcode')['ReadDepth'].sum()
xwsSamplesWithCoverage=sampleRdS.index[sampleRdS>=threshold]
m_base=wxsWithDataDf.index.get_level_values('base')==selectedBase
m_wxs_coverage=wxsWithDataDf.index.get_level_values('sample_barcode').isin(xwsSamplesWithCoverage)
m_valid_all=mergedDf.notnull().all(axis=1)
wxsWithDataDf_base=wxsWithDataDf[m_base&m_wxs_coverage]
wxsWithDataDf_base['rna-seq']=wxsWithDataDf_base['rna-seq'].fillna(0)
y_true=wxsWithDataDf_base['wxs']['ReadDepth']>=threshold
precision,recall,_=metrics.precision_recall_curve(y_true,
wxsWithDataDf_base['rna-seq']['ReadDepth'].fillna(0))
roc_auc=metrics.roc_auc_score(y_true,
wxsWithDataDf_base['rna-seq']['ReadDepth'].fillna(0))
auprc=metrics.auc(recall,precision)
#print (auprc,wxsWithDataDf_base['rna-seq']['ReadDepth'].fillna(0).mean())
myResultL=[{'auprc':auprc,'vcfIndex':vcfIndex,"rocauc":roc_auc,
'rnaseq_rd':sampleRdS_rnaseq.mean(),
'rnaseq_n':((sampleRdS_rnaseq>=10).sum())}]
roc_auc_l+= myResultL
print (myResultL)
successCount+=1
print (successCount)
except ValueError:#ValueError
failedS_L.append(vcfDfRowS)
print ('failed')
#group=wxsWithDataDf.groupby('base')
#for base, df in group:
# break
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9982105610204264, 'vcfIndex': ('2', 208248388), 'rocauc': 0.9842904603701946, 'rnaseq_rd': 133.82251908396947, 'rnaseq_n': 519}] 1
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.5436157339090322, 'vcfIndex': ('17', 7673803), 'rocauc': 0.9452658347625525, 'rnaseq_rd': 122.07633587786259, 'rnaseq_n': 520}] 2
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.8651493930905695, 'vcfIndex': ('2', 208248389), 'rocauc': 0.8964102564102564, 'rnaseq_rd': 133.3759541984733, 'rnaseq_n': 519}] 3
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9915456162454604, 'vcfIndex': ('14', 32092134), 'rocauc': 0.5077669902912622, 'rnaseq_rd': 38.31297709923664, 'rnaseq_n': 457}] 4
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9517857142857143, 'vcfIndex': ('2', 208248389), 'rocauc': 0.9577020202020201, 'rnaseq_rd': 133.3759541984733, 'rnaseq_n': 519}] 5
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 1.0, 'vcfIndex': ('15', 90088606), 'rocauc': 1.0, 'rnaseq_rd': 353.8416030534351, 'rnaseq_n': 524}] 6
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.954090909090909, 'vcfIndex': ('17', 7673802), 'rocauc': 0.9488888888888888, 'rnaseq_rd': 121.37284894837477, 'rnaseq_n': 520}] 7
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.7384169884169884, 'vcfIndex': ('8', 142877758), 'rocauc': 0.5, 'rnaseq_rd': 0.0019305019305019305, 'rnaseq_n': 0}] 8
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9895369944981679, 'vcfIndex': ('X', 24789042), 'rocauc': 0.5035885167464115, 'rnaseq_rd': 5.2629482071713145, 'rnaseq_n': 91}] 9
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9999400689281579, 'vcfIndex': ('1', 109690516), 'rocauc': 0.9965412883700822, 'rnaseq_rd': 210.7767175572519, 'rnaseq_n': 513}] 10
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9751543209876543, 'vcfIndex': ('17', 7674872), 'rocauc': 0.9993704752911552, 'rnaseq_rd': 59.13549618320611, 'rnaseq_n': 496}] 11 failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.6849247001118479, 'vcfIndex': ('6', 29944050), 'rocauc': 0.6133071391504189, 'rnaseq_rd': 16.24236641221374, 'rnaseq_n': 286}] 12
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 1.0, 'vcfIndex': ('2', 208248389), 'rocauc': 1.0, 'rnaseq_rd': 133.3759541984733, 'rnaseq_n': 519}] 13
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.998226347522553, 'vcfIndex': ('X', 24788994), 'rocauc': 0.6949317738791423, 'rnaseq_rd': 1291.3740458015268, 'rnaseq_n': 524}] 14
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9941271648588722, 'vcfIndex': ('12', 6018369), 'rocauc': 0.6216216216216216, 'rnaseq_rd': 36.32053742802303, 'rnaseq_n': 431}] 15
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.8950736763236764, 'vcfIndex': ('17', 7674220), 'rocauc': 0.9293664383561644, 'rnaseq_rd': 124.63671128107075, 'rnaseq_n': 520}] 16
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.8500000000000001, 'vcfIndex': ('17', 7675076), 'rocauc': 0.9983935742971888, 'rnaseq_rd': 91.69083969465649, 'rnaseq_n': 510}] 17
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.7798582995951417, 'vcfIndex': ('17', 7675088), 'rocauc': 0.7655677655677655, 'rnaseq_rd': 107.20537428023033, 'rnaseq_n': 509}] 18
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed failed failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9242947346041334, 'vcfIndex': ('12', 6018901), 'rocauc': 0.6154363110008272, 'rnaseq_rd': 79.05152671755725, 'rnaseq_n': 502}] 19
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.967687875497635, 'vcfIndex': ('6', 31271836), 'rocauc': 0.6717948717948719, 'rnaseq_rd': 950.9332061068702, 'rnaseq_n': 524}] 20
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.5249729346906801, 'vcfIndex': ('6', 31356729), 'rocauc': 0.4567348881485007, 'rnaseq_rd': 1370.7922330097088, 'rnaseq_n': 502}] 21 failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9664750957854407, 'vcfIndex': ('7', 117548682), 'rocauc': 0.5, 'rnaseq_rd': 0.39272030651340994, 'rnaseq_n': 1}] 22
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.8435959942590133, 'vcfIndex': ('6', 29943406), 'rocauc': 0.4709963985594237, 'rnaseq_rd': 2902.0687022900765, 'rnaseq_n': 522}] 23
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.6240315082644627, 'vcfIndex': ('6', 29943422), 'rocauc': 0.5176321912862072, 'rnaseq_rd': 2319.403474903475, 'rnaseq_n': 480}] 24
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9999999999999998, 'vcfIndex': ('17', 7674221), 'rocauc': 1.0, 'rnaseq_rd': 123.95602294455067, 'rnaseq_n': 520}] 25
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9769153916419274, 'vcfIndex': ('7', 142750675), 'rocauc': 0.49849488260084285, 'rnaseq_rd': 0.3199152542372881, 'rnaseq_n': 3}] 26
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.8815028901734103, 'vcfIndex': ('7', 152238825), 'rocauc': 0.5, 'rnaseq_rd': 9.790076335877863, 'rnaseq_n': 212}] 27
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.7770187787215652, 'vcfIndex': ('17', 7673776), 'rocauc': 0.8756735950731331, 'rnaseq_rd': 121.84351145038168, 'rnaseq_n': 518}] 28
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.5016891891891891, 'vcfIndex': ('9', 128257486), 'rocauc': 0.5, 'rnaseq_rd': 84.02579365079364, 'rnaseq_n': 472}] 29
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9621421257423716, 'vcfIndex': ('7', 142750600), 'rocauc': 0.5010526315789474, 'rnaseq_rd': 0.21595330739299612, 'rnaseq_n': 4}] 30
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.11665167191482981, 'vcfIndex': ('7', 55165350), 'rocauc': 0.6013007054673721, 'rnaseq_rd': 300.21946564885496, 'rnaseq_n': 481}] 31 failed failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9994991036591797, 'vcfIndex': ('12', 2685853), 'rocauc': 0.7816091954022988, 'rnaseq_rd': 2.092741935483871, 'rnaseq_n': 8}] 32
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9612392525801189, 'vcfIndex': ('4', 144120554), 'rocauc': 0.4796998031496063, 'rnaseq_rd': 0.49236641221374045, 'rnaseq_n': 3}] 33
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.8670477230214318, 'vcfIndex': ('6', 29944118), 'rocauc': 0.6404452281243111, 'rnaseq_rd': 18.980582524271846, 'rnaseq_n': 315}] 34 failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.8319444444444444, 'vcfIndex': ('17', 7674230), 'rocauc': 0.8713235294117647, 'rnaseq_rd': 120.80534351145039, 'rnaseq_n': 519}] 35
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.7957251082251082, 'vcfIndex': ('17', 7674945), 'rocauc': 0.869140625, 'rnaseq_rd': 99.9675572519084, 'rnaseq_n': 513}] 36
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9917339294729354, 'vcfIndex': ('19', 14766987), 'rocauc': 0.5071428571428571, 'rnaseq_rd': 1.315487571701721, 'rnaseq_n': 9}] 37
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.718190399137001, 'vcfIndex': ('7', 55154129), 'rocauc': 0.8454455445544554, 'rnaseq_rd': 182.2767175572519, 'rnaseq_n': 464}] 38
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9565217391304348, 'vcfIndex': ('7', 127611678), 'rocauc': 0.5, 'rnaseq_rd': 0.06451612903225806, 'rnaseq_n': 0}] 39
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9811409712399812, 'vcfIndex': ('1', 235775088), 'rocauc': 0.504950495049505, 'rnaseq_rd': 0.0136986301369863, 'rnaseq_n': 0}] 40
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9224825164827356, 'vcfIndex': ('1', 173828313), 'rocauc': 0.501444707118466, 'rnaseq_rd': 2.292089249492901, 'rnaseq_n': 1}] 41
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9913282738681911, 'vcfIndex': ('2', 166281810), 'rocauc': 0.5231741573033708, 'rnaseq_rd': 1.3317073170731708, 'rnaseq_n': 15}] 42
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9444444444444444, 'vcfIndex': ('6', 32664778), 'rocauc': 0.5, 'rnaseq_rd': 2.370212765957447, 'rnaseq_n': 8}] 43
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.07298916724566964, 'vcfIndex': ('6', 31270232), 'rocauc': 0.5693114455084359, 'rnaseq_rd': 747.1783567134269, 'rnaseq_n': 401}] 44
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.8904019236433559, 'vcfIndex': ('12', 52897420), 'rocauc': 0.5084404879657105, 'rnaseq_rd': 7.585603112840467, 'rnaseq_n': 71}] 45
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.559769267265185, 'vcfIndex': ('6', 29942825), 'rocauc': 0.797976477463657, 'rnaseq_rd': 2793.31106870229, 'rnaseq_n': 524}] 46
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.46834657753136016, 'vcfIndex': ('6', 29942845), 'rocauc': 0.4998989898989899, 'rnaseq_rd': 2905.9483747609943, 'rnaseq_n': 517}] 47
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9229132597203707, 'vcfIndex': ('6', 29944102), 'rocauc': 0.7980787271567413, 'rnaseq_rd': 21.58206106870229, 'rnaseq_n': 368}] 48
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.8023328381245963, 'vcfIndex': ('6', 29944103), 'rocauc': 0.7773660377358491, 'rnaseq_rd': 21.608778625954198, 'rnaseq_n': 371}] 49
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9422616789380488, 'vcfIndex': ('6', 29944168), 'rocauc': 0.9607098982098983, 'rnaseq_rd': 4361.543893129771, 'rnaseq_n': 524}] 50
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.5614637623652268, 'vcfIndex': ('12', 6018910), 'rocauc': 0.5450518969219758, 'rnaseq_rd': 73.97137404580153, 'rnaseq_n': 500}] 51 failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9961163900517636, 'vcfIndex': ('5', 236441), 'rocauc': 0.5004950495049505, 'rnaseq_rd': 189.5229007633588, 'rnaseq_n': 524}] 52
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.7945205479452055, 'vcfIndex': ('3', 10064460), 'rocauc': 0.5, 'rnaseq_rd': 0.26705653021442494, 'rnaseq_n': 0}] 53
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.5047709923664122, 'vcfIndex': ('3', 179199690), 'rocauc': 0.5, 'rnaseq_rd': 10.774809160305344, 'rnaseq_n': 237}] 54 failed failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/sklearn/metrics/ranking.py:444: RuntimeWarning: invalid value encountered in true_divide recall = tps / tps[-1]
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.8408395548245163, 'vcfIndex': ('6', 32661364), 'rocauc': 0.6422820109976433, 'rnaseq_rd': 113.46332046332046, 'rnaseq_n': 358}] 55
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9645215692947171, 'vcfIndex': ('6', 32661416), 'rocauc': 0.6010173721086477, 'rnaseq_rd': 214.6240458015267, 'rnaseq_n': 489}] 56
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.035856045886774615, 'vcfIndex': ('22', 42127537), 'rocauc': 0.4298987568883762, 'rnaseq_rd': 17.948374760994263, 'rnaseq_n': 355}] 57
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9957796476538225, 'vcfIndex': ('6', 32661360), 'rocauc': 0.4311175337186898, 'rnaseq_rd': 97.21606118546845, 'rnaseq_n': 337}] 58 failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9604493382073076, 'vcfIndex': ('6', 29943620), 'rocauc': 0.546979136482179, 'rnaseq_rd': 12.659655831739961, 'rnaseq_n': 238}] 59
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.7750889986870693, 'vcfIndex': ('6', 29944059), 'rocauc': 0.6722366428725935, 'rnaseq_rd': 17.18320610687023, 'rnaseq_n': 315}] 60
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
[{'auprc': 0.9842224503338726, 'vcfIndex': ('6', 29944067), 'rocauc': 0.8036034099863886, 'rnaseq_rd': 16.535372848948374, 'rnaseq_n': 315}] 61
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:27: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:49: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:73: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
failed
praucDf=pd.DataFrame(roc_auc_l).dropna().head(n=100)#.to_frame('prauc')
praucDf
auprc | rnaseq_n | rnaseq_rd | rocauc | vcfIndex | |
---|---|---|---|---|---|
0 | 0.998211 | 519 | 133.822519 | 0.984290 | (2, 208248388) |
1 | 0.543616 | 520 | 122.076336 | 0.945266 | (17, 7673803) |
2 | 0.865149 | 519 | 133.375954 | 0.896410 | (2, 208248389) |
3 | 0.991546 | 457 | 38.312977 | 0.507767 | (14, 32092134) |
4 | 0.951786 | 519 | 133.375954 | 0.957702 | (2, 208248389) |
5 | 1.000000 | 524 | 353.841603 | 1.000000 | (15, 90088606) |
6 | 0.954091 | 520 | 121.372849 | 0.948889 | (17, 7673802) |
7 | 0.738417 | 0 | 0.001931 | 0.500000 | (8, 142877758) |
8 | 0.989537 | 91 | 5.262948 | 0.503589 | (X, 24789042) |
9 | 0.999940 | 513 | 210.776718 | 0.996541 | (1, 109690516) |
10 | 0.975154 | 496 | 59.135496 | 0.999370 | (17, 7674872) |
11 | 0.684925 | 286 | 16.242366 | 0.613307 | (6, 29944050) |
12 | 1.000000 | 519 | 133.375954 | 1.000000 | (2, 208248389) |
13 | 0.998226 | 524 | 1291.374046 | 0.694932 | (X, 24788994) |
14 | 0.994127 | 431 | 36.320537 | 0.621622 | (12, 6018369) |
15 | 0.895074 | 520 | 124.636711 | 0.929366 | (17, 7674220) |
16 | 0.850000 | 510 | 91.690840 | 0.998394 | (17, 7675076) |
17 | 0.779858 | 509 | 107.205374 | 0.765568 | (17, 7675088) |
18 | 0.924295 | 502 | 79.051527 | 0.615436 | (12, 6018901) |
19 | 0.967688 | 524 | 950.933206 | 0.671795 | (6, 31271836) |
20 | 0.524973 | 502 | 1370.792233 | 0.456735 | (6, 31356729) |
21 | 0.966475 | 1 | 0.392720 | 0.500000 | (7, 117548682) |
22 | 0.843596 | 522 | 2902.068702 | 0.470996 | (6, 29943406) |
23 | 0.624032 | 480 | 2319.403475 | 0.517632 | (6, 29943422) |
24 | 1.000000 | 520 | 123.956023 | 1.000000 | (17, 7674221) |
25 | 0.976915 | 3 | 0.319915 | 0.498495 | (7, 142750675) |
26 | 0.881503 | 212 | 9.790076 | 0.500000 | (7, 152238825) |
27 | 0.777019 | 518 | 121.843511 | 0.875674 | (17, 7673776) |
28 | 0.501689 | 472 | 84.025794 | 0.500000 | (9, 128257486) |
29 | 0.962142 | 4 | 0.215953 | 0.501053 | (7, 142750600) |
... | ... | ... | ... | ... | ... |
70 | 0.002137 | 16 | 2.042345 | 0.495708 | (1, 237591774) |
71 | 0.808434 | 524 | 3416.650763 | 0.442027 | (6, 29944376) |
72 | 0.232668 | 524 | 3618.646947 | 0.603043 | (6, 29944151) |
73 | 0.741291 | 506 | 315.198473 | 0.621487 | (6, 32664883) |
74 | 0.026316 | 436 | 162.306796 | 0.784810 | (6, 32664926) |
75 | 0.863203 | 395 | 31.936902 | 0.488386 | (10, 4999206) |
76 | 0.815908 | 493 | 215.211832 | 0.928361 | (6, 32661393) |
77 | 0.380747 | 480 | 191.682692 | 0.596527 | (6, 32661384) |
78 | 0.778990 | 27 | 2.581081 | 0.645061 | (6, 32661333) |
79 | 0.007407 | 0 | 1.307692 | 0.481203 | (12, 57099758) |
80 | 0.641934 | 524 | 353.841603 | 0.795312 | (15, 90088606) |
81 | 0.993934 | 523 | 1127.133588 | 0.582806 | (16, 2106849) |
82 | 0.995522 | 517 | 1391.395753 | 0.989221 | (6, 29942795) |
83 | 0.965023 | 510 | 2437.399610 | 0.856497 | (6, 29942858) |
84 | 0.061988 | 524 | 2200.085878 | 0.573877 | (6, 29942916) |
85 | 0.756602 | 29 | 2.614504 | 0.669605 | (3, 75630855) |
86 | 0.224100 | 13 | 1.728489 | 0.588009 | (3, 75630794) |
87 | 0.549532 | 103 | 7.149510 | 0.523889 | (3, 49686483) |
88 | 0.683612 | 519 | 1443.973282 | 0.499179 | (6, 29943463) |
89 | 0.758810 | 35 | 3.059961 | 0.520303 | (6, 29943667) |
90 | 0.858112 | 523 | 66.984733 | 0.899413 | (3, 179234284) |
91 | 0.844742 | 513 | 88.143130 | 0.874750 | (17, 7674888) |
92 | 1.000000 | 517 | 117.526718 | 1.000000 | (17, 7674256) |
93 | 0.493328 | 512 | 82.120229 | 0.692187 | (17, 7673704) |
94 | 0.403970 | 55 | 3.786275 | 0.490953 | (17, 21416556) |
95 | 0.666459 | 523 | 986.114504 | 0.500538 | (8, 100709671) |
96 | 0.951125 | 0 | 0.047244 | 0.509217 | (3, 183959847) |
97 | 0.671406 | 501 | 94.854127 | 0.794175 | (17, 31350209) |
98 | 0.530668 | 518 | 380.994275 | 0.738304 | (5, 68295269) |
99 | 0.870781 | 495 | 23.572519 | 0.462571 | (22, 24627926) |
100 rows × 5 columns
(praucDf['auprc']<0.1).mean()
0.09
(praucDf['auprc']>0.8).mean()
0.73
praucDf.head()
auprc | rnaseq_n | rnaseq_rd | vcfIndex | |
---|---|---|---|---|
0 | 0.998211 | 519 | 133.822519 | (2, 208248388) |
1 | 0.543616 | 520 | 122.076336 | (17, 7673803) |
2 | 0.865149 | 519 | 133.375954 | (2, 208248389) |
3 | 0.991546 | 448 | 38.312977 | (14, 32092134) |
4 | 0.951786 | 519 | 133.375954 | (2, 208248389) |
import matplotlib.pyplot as plt
fig,ax=plt.subplots(figsize=(4,3))
praucDf['auprc'].hist(ax=ax)
#ax.set_yticklabels([])
ax.grid(False)
ax.set_yticklabels([])
ax.set_ylabel('# of samples')
ax.set_xlabel('AUPRC')
Text(0.5,0,'AUPRC')
praucS=pd.Series(roc_auc_l).dropna()
(praucS>0.8).mean()
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-189-913ac00a7691> in <module>() 1 praucS=pd.Series(roc_auc_l).dropna() ----> 2 (praucS>0.8).mean() ~/anaconda3/lib/python3.6/site-packages/pandas/core/ops.py in wrapper(self, other, axis) 1251 1252 with np.errstate(all='ignore'): -> 1253 res = na_op(values, other) 1254 if is_scalar(res): 1255 raise TypeError('Could not compare {typ} type with Series' ~/anaconda3/lib/python3.6/site-packages/pandas/core/ops.py in na_op(x, y) 1138 1139 elif is_object_dtype(x.dtype): -> 1140 result = _comp_method_OBJECT_ARRAY(op, x, y) 1141 1142 elif is_datetimelike_v_numeric(x, y): ~/anaconda3/lib/python3.6/site-packages/pandas/core/ops.py in _comp_method_OBJECT_ARRAY(op, x, y) 1117 result = libops.vec_compare(x, y, op) 1118 else: -> 1119 result = libops.scalar_compare(x, y, op) 1120 return result 1121 pandas/_libs/ops.pyx in pandas._libs.ops.scalar_compare() TypeError: '>' not supported between instances of 'dict' and 'float'
ax=pd.Series(roc_auc_l).hist(normed=True)
ax
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/matplotlib/axes/_axes.py:6462: UserWarning: The 'normed' kwarg is deprecated, and has been replaced by the 'density' kwarg. warnings.warn("The 'normed' kwarg is deprecated, and has been "
--------------------------------------------------------------------------- TypeError Traceback (most recent call last) <ipython-input-182-d7534bb7361c> in <module>() ----> 1 ax=pd.Series(roc_auc_l).hist(normed=True) 2 ax ~/anaconda3/lib/python3.6/site-packages/pandas/plotting/_core.py in hist_series(self, by, ax, grid, xlabelsize, xrot, ylabelsize, yrot, figsize, bins, **kwds) 2479 values = self.dropna().values 2480 -> 2481 ax.hist(values, bins=bins, **kwds) 2482 ax.grid(grid) 2483 axes = np.array([ax]) ~/anaconda3/lib/python3.6/site-packages/matplotlib/__init__.py in inner(ax, *args, **kwargs) 1853 "the Matplotlib list!)" % (label_namer, func.__name__), 1854 RuntimeWarning, stacklevel=2) -> 1855 return func(ax, *args, **kwargs) 1856 1857 inner.__doc__ = _add_data_doc(inner.__doc__, ~/anaconda3/lib/python3.6/site-packages/matplotlib/axes/_axes.py in hist(***failed resolving arguments***) 6512 for xi in x: 6513 if len(xi) > 0: -> 6514 xmin = min(xmin, xi.min()) 6515 xmax = max(xmax, xi.max()) 6516 bin_range = (xmin, xmax) TypeError: '<' not supported between instances of 'dict' and 'float'
wxsWithDataDf_base.head()
rna-seq | wxs | ||||||
---|---|---|---|---|---|---|---|
features | ReadDepth | AverageBaseQuality | ReadDepth | AverageBaseQuality | |||
sample_barcode | Chr | Pos | base |
threshold=2
selectedBase='T'
query_chromosome, qeury_corrdinate='2',208248388
m_chr=targetted_df.index.get_level_values('Chr')==query_chromosome
Pos_array=targetted_df.index.get_level_values('Pos')
window_size=0
m_pos=(Pos_array>=(qeury_corrdinate-window_size))&(Pos_array<=(qeury_corrdinate+window_size))
m_qual=targetted_df['AverageBaseQuality']>=30
targetted_df_sub=targetted_df[m_pos&m_qual]
index_metaDf=targetted_df_sub.index.to_frame()
index_metaDf['sample_barcode']=manifest_df_w_RNA_WXS.set_index('file_id').loc[index_metaDf['Run_digits']]['sample_barcode'].values
multI=index_metaDf.set_index(['sample_barcode','Run_digits','Chr','Pos','base']).index
targetted_df_sub.index=multI
rnaseq_uuids=manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS['experimental_strategy']=='RNA-Seq']['file_id'].unique()
m_uuid=targetted_df_sub.index.get_level_values('Run_digits').isin(rnaseq_uuids)
rnaseq_df=targetted_df_sub[m_uuid]
groupings_L=['sample_barcode','Chr','Pos','base']
rnaseq_df=rnaseq_df.groupby(groupings_L).first()
wxs_uuids=manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS['experimental_strategy']=='WXS']['file_id'].unique()
m_uuid=targetted_df_sub.index.get_level_values('Run_digits').isin(wxs_uuids)
wxs_df=targetted_df_sub[m_uuid]
wxs_df=wxs_df.groupby(groupings_L).first()
mergedDf=pd.concat([ rnaseq_df,wxs_df],axis=1,keys=['rna-seq','wxs'])
mergedDf['wxs']['ReadDepth']=mergedDf['wxs']['ReadDepth'].fillna(0)
#mergedDf
#for the whole
from sklearn import metrics
#### get the homozygous
wxsWithDataDf=mergedDf#[mergedDf['wxs']['ReadDepth']>=threshold]
sampleRdS=wxsWithDataDf['wxs'].groupby('sample_barcode')['ReadDepth'].sum()
xwsSamplesWithCoverage=sampleRdS.index[sampleRdS>threshold]
m_base=wxsWithDataDf.index.get_level_values('base')==selectedBase
m_wxs_coverage=wxsWithDataDf.index.get_level_values('sample_barcode').isin(xwsSamplesWithCoverage)
m_valid_all=mergedDf.notnull().all(axis=1)
wxsWithDataDf_base=wxsWithDataDf[m_base&m_wxs_coverage]
wxsWithDataDf_base['rna-seq']=wxsWithDataDf_base['rna-seq'].fillna(0)
#wxsWithDataDf_base['rna-seq']['ReadDepth'].hist()
#wxsWithDataDf_base['wxs']['ReadDepth'].hist()
y_true=wxsWithDataDf_base['wxs']['ReadDepth']>=threshold
precision,recall,_=metrics.precision_recall_curve(y_true,
wxsWithDataDf_base['rna-seq']['ReadDepth'].fillna(0))
auprc=metrics.auc(recall,precision)
#group=wxsWithDataDf.groupby('base')
#for base, df in group:
# break
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:13: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike del sys.path[0] /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:35: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy /cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:62: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame. Try using .loc[row_indexer,col_indexer] = value instead See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
index_metaDf=targetted_df_sub.index.to_frame()
index_metaDf['sample_barcode']=manifest_df_w_RNA_WXS.set_index('file_id').loc[index_metaDf['Run_digits']]['sample_barcode'].values
multI=index_metaDf.set_index(['sample_barcode','Run_digits','Chr','Pos','base']).index
targetted_df_sub.index=multI
wxs_df=targetted_df_sub[m_uuid]#.loc[wxs_uuid]
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:3: FutureWarning: Passing list-likes to .loc or [] with any missing label will raise KeyError in the future, you can use .reindex() as an alternative. See the documentation here: https://pandas.pydata.org/pandas-docs/stable/indexing.html#deprecate-loc-reindex-listlike This is separate from the ipykernel package so we can avoid doing imports until
%time wxs_df=wxs_df.groupby(groupings_L).first()
CPU times: user 72 ms, sys: 32 ms, total: 104 ms Wall time: 102 ms
rnaseq_uuids=manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS['experimental_strategy']=='RNA-Seq']['file_id'].unique()
m_uuid=targetted_df_sub.index.get_level_values('Run_digits').isin(rnaseq_uuids)
rnaseq_df=targetted_df_sub[m_uuid]#.loc[rnaseq_uuid]
%time rnaseq_df=rnaseq_df.groupby(groupings_L).first()
CPU times: user 24 ms, sys: 0 ns, total: 24 ms Wall time: 28.5 ms
mergedDf=pd.concat([ rnaseq_df,wxs_df],axis=1,keys=['rna-seq','wxs'])
mergedDf=mergedDf[~mergedDf.isnull().all(axis=1)]
#ref C
IDH1_corrdinate=208248388
mergedDf_subDf=mergedDf[mergedDf.index.get_level_values('Pos')==IDH1_corrdinate]
m_quality=(mergedDf_subDf['wxs']['AverageBaseQuality']>20)
ref_alt='T'
m_alt=(mergedDf_subDf.index.get_level_values('base'))==ref_alt
qualFilteredDf=mergedDf_subDf[m_quality]
unstackDf=qualFilteredDf.unstack()
unstackDf.head()
rna-seq | wxs | |||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
features | ReadDepth | AverageBaseQuality | ReadDepth | AverageBaseQuality | ||||||||||||||
base | A | C | G | T | A | C | G | T | A | C | G | T | A | C | G | T | ||
sample_barcode | Chr | Pos | ||||||||||||||||
TCGA-CS-4938-01B | 2 | 208248388 | NaN | 68.0 | NaN | 24.0 | NaN | 37.0 | NaN | 38.0 | NaN | 87.0 | NaN | 29.0 | NaN | 29.0 | NaN | 29.0 |
TCGA-CS-4941-01A | 2 | 208248388 | NaN | 235.0 | NaN | NaN | NaN | 37.0 | NaN | NaN | NaN | 182.0 | NaN | NaN | NaN | 27.0 | NaN | NaN |
TCGA-CS-4942-01A | 2 | 208248388 | NaN | 140.0 | NaN | 19.0 | NaN | 38.0 | NaN | 38.0 | NaN | 192.0 | NaN | 46.0 | NaN | 25.0 | NaN | 28.0 |
TCGA-CS-4944-01A | 2 | 208248388 | NaN | 43.0 | NaN | 17.0 | NaN | 37.0 | NaN | 37.0 | NaN | 149.0 | NaN | 43.0 | NaN | 27.0 | NaN | 28.0 |
TCGA-CS-5390-01A | 2 | 208248388 | NaN | 95.0 | NaN | 32.0 | NaN | 37.0 | NaN | 38.0 | NaN | 141.0 | NaN | 51.0 | NaN | 26.0 | NaN | 27.0 |
from sklearn import metrics
import matplotlib.pyplot as plt
fig,ax=plt.subplots(figsize=(5,3))
unstackDf[('wxs','ReadDepth','T')].fillna(0).hist(bins=30,label='Minor alle',ax=ax)
unstackDf[('wxs','ReadDepth','C')].fillna(0).hist(bins=30,ax=ax,
label='Reference allele')
ax.axvline(x=10,c='red')
ax.set_ylabel('# of tumor samples')
ax.legend()
ax.set_xlabel('Allelic read counts')
ax.grid(False)
(unstackDf[('wxs','ReadDepth','T')]>0).sum()
351
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--------------------------------------------------------------------------- NameError Traceback (most recent call last) <ipython-input-41-61aacb46f36f> in <module>() ----> 1 asdasdas NameError: name 'asdasdas' is not defined
y_true=(>10)
y_true.value_counts()
print ('ROC AUC',metrics.roc_auc_score(y_true,
unstackDf[('rna-seq','ReadDepth','T')].fillna(0)))
precision, recall, thresholds=metrics.precision_recall_curve(y_true,
unstackDf[('rna-seq','ReadDepth','T')].fillna(0))
ax=pd.DataFrame({'precision':precision,'recall':recall}).plot(x='recall',y='precision')
ax.set_ylabel('Precision')
ax.set_xlabel('Recall')
metrics.auc(recall,precision)
ax.set_title('IDH1 C>T mutation using RNAseq')
import seaborn as sns
qualFilteredDf[('wxs','ReadDepth')].index.get_level_values('base').value_counts()
qualFilteredDf[('rna-seq','ReadDepth')].index.get_level_values('base').value_counts()
qualFilteredDf[('rna-seq','ReadDepth')].index.get_level_values('base').value_counts()
mergedDf_subDf
qualFilteredDf['ReadDepth'],qualFilteredDf['wxs']>3
##c
#qualFilteredDf[]
unstackDf=qualFilteredDf['wxs'].unstack()['ReadDepth']
#qualFilteredDf['wxs'].unstack()['ReadDepth']
sns.jointplot(data=qualFilteredDf[qualFilteredDf.index.get_level_values('base')=='T'],x=('rna-seq','ReadDepth'),y=('wxs','ReadDepth'))
#categorical_crossentropy
### generate the correlation between the data