does not start column index a 0

bin/merge_cols.py

@@ -32,7 +32,7 @@ __authors__ = "Celine Noirot"
 __keywords__ = "Count matrix, join columns, merge files"
 __description__ = "Merge (join) files columns on first column, skip lines starting with #"
 
-def read_file (file,libname,dict_col, col_number=1):
+def read_file (file,libname,dict_col, col_number=2):
     """
     Extract count from the count file 
       @param file          : the input count file (output of sam2count)
@@ -71,7 +71,7 @@ parser = OptionParser(usage="Usage: %prog", description = "Merge files columns o
 igroup = OptionGroup(parser, "Input options","")
 igroup.add_option("-f", "--files", dest="files", help="tabulated files separated by ',' ")
 igroup.add_option("-n", "--names", dest="names", help="matrix columns names in the same order as files ',' ")
-igroup.add_option("-c", "--column", dest="col_number", help="column of each files to extract, first column is 0, default 1", default=1, metavar="INT")
+igroup.add_option("-c", "--column", dest="col_number", help="column of each files to extract, first column is 1, default 2", default=2, metavar="INT")
 parser.add_option_group(igroup)
 
 ogroup = OptionGroup(parser, "Output files options","")
@@ -85,8 +85,8 @@ if options.files == None :
     parser.print_help()
     sys.exit(1)
 
-if options.col_number < 1 :
-    sys.stderr.write("Column must be greater than 0 \n")
+if int(options.col_number) < 2 :
+    sys.stderr.write("Column must be greater than 1 \n")
     parser.print_help()
     sys.exit(1)
     
@@ -107,6 +107,7 @@ if options.names :
          parser.print_help()
          sys.exit(1)
 
+col_to_extract=int(options.col_number)-1
 current_libname=""
 for idx, line in enumerate(files):        
     file = line.rstrip()
@@ -116,12 +117,12 @@ for idx, line in enumerate(files):
             libs_name.append(current_libname)
         else : 
             current_libname = libs_name[idx]
-        read_file(file,current_libname,dict_col,options.col_number)
+        read_file(file,current_libname,dict_col,col_to_extract)
     else :
         sys.stderr.write("File : " + file + " doesn't exist")
         sys.exit(1)
 fout = open (options.output,"w")
-fout.write ( '#contig_name\t' + '\t'.join(libs_name) +"\n")
+fout.write ( '#id\t' + '\t'.join(libs_name) +"\n")
 # Pour tous les contigs : contruction de la ligne 
 for contig_name in sorted(dict_col.keys()) :
     line = []
@@ -132,4 +133,4 @@ for contig_name in sorted(dict_col.keys()) :
     fout.write ( '\t'.join(line) +"\n")
 fout.close
 sys.exit(0)
-        
\ No newline at end of file
+