argparse system and many markers

scripts/prepare_spygen_data.py

 import pandas
 import sys
+import argparse
+import os
 
-datFile='Teleo.dat'
-aliceFile='cor_tag_teleo.csv'
+#datFile='Teleo.dat'
+#aliceFile='cor_tag_teleo.csv'
+#projetName='notreProjet'
+
+parser = argparse.ArgumentParser(description='prepare rapidrun allsamples CSV file')
+parser.add_argument("-d","--datFolder", type=str, help="Folder of the dat files")
+parser.add_argument("-a","--aliceFile", type=str, help="CSV Alice file")
+parser.add_argument("-p","--projetName", type=str, help="name of the project")
+args = parser.parse_args()
+
+datFolder = args.datFolder
+aliceFile = args.aliceFile
+projetName = args.projetName
+
+
+datFolder='resources/test/test_rapidrun_data/ngs/rapidrun_metadata/'
+
+datFolderList = os.listdir(datFolder)
+datFiles = {}
+for fichier in datFolderList:
+    if ".dat" in fichier:
+        datMarker = fichier.split(".")[0].lower()
+        datFiles[datMarker]= datFolder+"/"+fichier
+datDic = {}
+for key in datFiles:
+    datDic[key] = pandas.read_csv(datFiles[key], sep='\t', names=["plaque", "plaque1", "tag", "primerF","primerR", "description"])
 
 
 ###############################################################################
@@ -10,7 +36,6 @@ aliceFile='cor_tag_teleo.csv'
 alice = pandas.read_csv(aliceFile, sep=';')
 dat = pandas.read_csv(datFile, sep='\t', names=["plaque", "plaque1", "tag", "primerF","primerR", "description"])
 
-
 uniqMarkers=alice.marker.unique()
 
 for marker in uniqMarkers:
@@ -32,11 +57,11 @@ for marker in uniqMarkers:
                     plaque = dat['plaque'][i]
                     sample = aliceRun['Sample'][j]
                     if "SPY" in sample:
-                        projet="notreProjet"
-                    elif "Other" in sample:
+                        projet=projetName
+                    elif "Other" in sample or "OTHER" in sample or "Other" in sample:
                         projet="Other"
                     else:
-                        projet="notreProjet"
+                        projet=projetName
                     print(plaque, run, sample, projet, marker, sep=";")
                     break
             if not in_alice: