import pandas as pd
gdc_meta_df=pd.read_json('files.2018-07-11.json')
#gdc_meta_df['cases']
#!cp ../XGS_WGS/ParseBamReadCount_base_case.ipynb ./TestPipeline/.
from tqdm import tqdm
#tqdm()
!grep -rn readcount ../**/*.ipynb
../XGS_WGS/testOne.ipynb:19: "bam_read_count_dir='/cellar/users/btsui/Program/bam_read_count/bam-readcount-master/bin/bam-readcount'\n", ../XGS_WGS/testOne.ipynb:115: "'/cellar/users/btsui/Program/bam_read_count/bam-readcount-master/bin/bam-readcount C494.TCGA-S9-A6U1-01A-21D-A33T-08.1_gdc_realn.bam |gzip > tcga.txt.gz'" ../XGS_WGS/testOne.ipynb:137: "'/cellar/users/btsui/Program/bam_read_count/bam-readcount-master/bin/bam-readcount -l /cellar/users/btsui/Data/dbsnp/snp_beds/Homo_sapiens.bed -f /cellar/users/btsui/Data/ensembl/snp_masked/Homo_sapiens.microbe.fa file_sorted |gzip > snp.txt.gz'" ../XGS_WGS/testOne.ipynb:394: "bam_read_count_dir='/cellar/users/btsui/Program/bam_read_count/bam-readcount-master/bin/bam-readcount'" ../XGS_WGS/testOne.ipynb:434: "'/cellar/users/btsui/Program/bam_read_count/bam-readcount-master/bin/bam-readcount -l loci.txt -f /cellar/users/btsui/Data/ensembl/snp_masked/Homo_sapiens.GRCh38.dna_rm.toplevel.SNP_masked.fa sorted.bam'" ../XGS_WGS/testOne.ipynb:443: "#bam-readcount -f ref.fa some.bam\n",
!grep -rn jointplot ../**/*.ipynb
../Analysis/CompareTCGA_alignment_w_mine_pipe.ipynb:246: "g=sns.jointplot(data=inPlotDf,x=ctrl_label,y=case_label,kind='hex',xlim=[0,10],ylim=[0,10])\n", ../Analysis/CompareTCGA_alignment_w_mine_pipe.ipynb:339: "g=sns.jointplot(data=inPlotDf2,x=ctrl_label,y=case_label,kind='hex',xlim=[0,10],ylim=[0,10])\n", ../Analysis/analyzeAnlignmentStatistics.ipynb:240: "h=sns.jointplot(data=unstackDf[unstackDf.aligned_reads_log10>3],x='aligned_reads_log10',\n", ../BS_aling/Untitled.ipynb:233: "sns.jointplot(data=myDf,x='rapmap',y='roadmap',kind='hex',stat_func=stats.spearmanr)" ../Chip-seq/CorrelateData.ipynb:520: "sns.jointplot(data=nonZeroDf,x='my pipline',y='epigenome roadmap pipeline',kind='scatter',size=5)" ../XGS_WGS/MaskingGenomeWithSnp_Specie.ipynb:1837: "sns.jointplot(data=np.log10(tmpDf+1),x='one',y='hundred')"