Develop

workflow/scripts/modifyFetch.py

-#!/usr/bin/env python3
-
-import argparse
-import pandas as pd
-import re
-
-def get_args():
-    parser = argparse.ArgumentParser()
-    parser.add_argument('-f', '--fetchFile',help="The fetch file from bdgap.zip.",required=True)
-    args = parser.parse_args()
-    return args
-
-def main():
-    args = get_args()
-    fetchFile = pd.read_csv(args.fetchFile+"/fetch.txt",sep="\t",header=None)
-    fileFile = pd.read_csv(args.fetchFile+"/data/File.csv",sep=",",header=0)
-    fileFile_filtered = fileFile[fileFile["File_Type"]=="FastQ"]
-    fetchFile_filtered = fetchFile[fetchFile[2].str[-9:]==".fastq.gz"]
-    fetchFile_filtered_renamed = fetchFile_filtered
-    for i in fileFile_filtered["File_Name"]:
-        fetchFile_filtered_renamed[2][fetchFile_filtered_renamed[2].str.contains(i,regex=False)] = fetchFile_filtered_renamed[2][fetchFile_filtered_renamed[2].str.contains(i,regex=False)].values[0].replace(re.sub("\.R.\.fastq\.gz","",i),fileFile_filtered["Replicate_RID"][fileFile_filtered["File_Name"]==i].values[0])
-    fetchFile_filtered_renamed.to_csv(args.fetchFile+"/fetch.txt",sep="\t",header=False,index=False)
-
-if __name__ == '__main__':
-    main()
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