%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
#targetted_df.head()
### use andrea mapping to map from TCGA barcode to UUID.
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()
with_both=tmpVC.index[tmpVC==2]
len(with_both)
524
manifest_df_w_RNA_WXS=manifest_df_sub[manifest_df_sub.sample_barcode.isin(with_both)]
#g=manifest_df_w_RNA_WXS.groupby(['sample_barcode','experimental_strategy'])
#[manifest_df_sub['sample_barcode']=='TCGA-HT-A4DV-01A']
#manifest_df_sub
#queryBarcode='TCGA-HT-A4DV-01A'
#rnaseq_uuid=g.get_group((queryBarcode,'RNA-Seq'))['file_id'].iloc[0]
#wxs_uuid=g.get_group((queryBarcode,'WXS'))['file_id'].iloc[0]
rnaseq_uuids=manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS['experimental_strategy']=='WXS']['file_id'].unique()
targetted_df.head()
features | ReadDepth | AverageBaseQuality | |||
---|---|---|---|---|---|
Run_digits | Chr | Pos | base | ||
08ce1dd9-3167-4fe4-8619-724727a32a36 | 1 | 14727 | A | 18 | 28 |
G | 280 | 32 | |||
630825 | T | 11 | 32 | ||
630833 | C | 9 | 34 | ||
833068 | G | 2 | 34 |
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')
varscanVcfMerged.head()
Group | one_vcf_df | ... | normal_df | INFO | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
VCF_columns | index | CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | ... | DP | RD | AD | FREQ | DP4 | DP | GPV | SPV | SS | SSC | ||
TUMOR | NORMAL | ||||||||||||||||||||||
TCGA-DU-5870-01A-11D-1705-08 | TCGA-DU-5870-10A-01D-1705-08 | 0 | 0 | chr1 | 944131 | . | A | C | . | PASS | DP=89;GPV=1E0;SOMATIC;SPV=5.0789E-2;SS=2;SSC=12 | GT:GQ:DP:RD:AD:FREQ:DP4 | ... | 20 | 18 | 2 | 10% | 8,10,0,2 | 89 | 1E0 | 5.0789E-2 | 2 | 12 |
1 | 1 | chr1 | 944136 | . | T | C | . | PASS | DP=92;GPV=1E0;SOMATIC;SPV=1.8932E-2;SS=2;SSC=17 | GT:GQ:DP:RD:AD:FREQ:DP4 | ... | 25 | 22 | 3 | 12% | 10,12,0,3 | 92 | 1E0 | 1.8932E-2 | 2 | 17 | ||
2 | 2 | chr1 | 1300684 | . | C | A | . | PASS | DP=71;GPV=1E0;SOMATIC;SPV=6.3354E-2;SS=2;SSC=11 | GT:GQ:DP:RD:AD:FREQ:DP4 | ... | 18 | 16 | 2 | 11.11% | 7,9,0,2 | 71 | 1E0 | 6.3354E-2 | 2 | 11 | ||
3 | 3 | chr1 | 1713611 | . | C | T | . | PASS | DP=59;GPV=1E0;SOMATIC;SPV=4.5001E-3;SS=2;SSC=23 | GT:GQ:DP:RD:AD:FREQ:DP4 | ... | 14 | 8 | 5 | 38.46% | 5,3,1,4 | 59 | 1E0 | 4.5001E-3 | 2 | 23 | ||
4 | 4 | chr1 | 1713674 | . | T | C | . | PASS | DP=42;GPV=1E0;SOMATIC;SPV=3.252E-2;SS=2;SSC=14 | GT:GQ:DP:RD:AD:FREQ:DP4 | ... | 8 | 6 | 2 | 25% | 0,6,0,2 | 42 | 1E0 | 3.252E-2 | 2 | 14 |
5 rows × 31 columns
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)]
querySample='TCGA-HT-A4DV-01A'
manifest_df_w_RNA_WXS[manifest_df_w_RNA_WXS.sample_barcode==querySample]
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 |
697 | controlled | NaN | [{'project': {'project_id': 'TCGA-LGG'}, 'case... | Raw Sequencing Data | BAM | Aligned Reads | WXS | f36d778a-2c49-43aa-a577-7a6a921ad6cc | C494.TCGA-HT-A4DV-01A-11D-A26M-08.4_gdc_realn.bam | 4776368233 | Illumina | True | TCGA-HT-A4DV-01A |
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]
targetted_df.head()
features | ReadDepth | AverageBaseQuality | |||
---|---|---|---|---|---|
Run_digits | Chr | Pos | base | ||
08ce1dd9-3167-4fe4-8619-724727a32a36 | 1 | 14727 | A | 18 | 28 |
G | 280 | 32 | |||
630825 | T | 11 | 32 | ||
630833 | C | 9 | 34 | ||
833068 | G | 2 | 34 |
wxsTargettedDf=targetted_df.loc[wxsUUID].reset_index().set_index(['Chr','Pos'])
wxsChrPosCountS=wxsTargettedDf.groupby(['Chr','Pos']).size()
#wxsTargettedDf
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.shape
(181591, 3)
wxsTargettedDf_homo['is_ref_base']=wxsTargettedDf_homo.index.isin(refI)
(~wxsTargettedDf_homo['is_ref_base']).mean()
0.10664625449499149
homoGermlineVariantDf=wxsTargettedDf_homo[(~wxsTargettedDf_homo['is_ref_base'])&(germlineVariantDf['ReadDepth']>=2)&(germlineVariantDf['AverageBaseQuality'])]
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/ipykernel_launcher.py:1: UserWarning: Boolean Series key will be reindexed to match DataFrame index. """Entry point for launching an IPython kernel.
homoGermlineVariantDf.shape
(15630, 3)
For homozygous germ line variants, only the reference allele are supposed to be detected
Exmaple: 7957 overlaping
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)
4543
homoGermlineVariantDf.head()
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 |
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]
germLineDf['AllelicFract'][germLineDf['AllelicFract']>0.995].hist()
<matplotlib.axes._subplots.AxesSubplot at 0x2b655d3820b8>
len(homoGermlineVariantDf.index)
15630
(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
asdasdas
--------------------------------------------------------------------------- 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