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Resolve "process_getData"

Merged Gervaise Henry requested to merge 1-process_getData into develop
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@@ -2,6 +2,7 @@
@@ -2,6 +2,7 @@
import argparse
import argparse
import pandas as pd
import pandas as pd
 
import re
def get_args():
def get_args():
parser = argparse.ArgumentParser()
parser = argparse.ArgumentParser()
@@ -12,8 +13,13 @@ def get_args():
@@ -12,8 +13,13 @@ def get_args():
def main():
def main():
args = get_args()
args = get_args()
fetchFile = pd.read_csv(args.fetchFile+"/fetch.txt",sep="\t",header=None)
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 = fetchFile[fetchFile[2].str[-9:]==".fastq.gz"]
fetchFile_filtered.to_csv(args.fetchFile+"/fetch.txt",sep="\t",header=False,index=False)
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__':
if __name__ == '__main__':
main()
main()
 
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