Debug _main_

bin/merge_cols.py

@@ -15,6 +15,10 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 #
 
+from optparse import *
+import sys,re,datetime
+from os.path import join, splitext, basename, exists, split
+
 __author__ = 'Plateforme bioinformatique Midi Pyrenees'
 __copyright__ = 'Copyright (C) 2009 INRA'
 __license__ = 'GNU General Public License'
@@ -28,10 +32,6 @@ __authors__ = "Celine Noirot"
 __keywords__ = "Count matrix, join columns, merge files"
 __description__ = "Merge (join) files columns on first column, skip lines starting with #"
 
-from optparse import *
-import sys,re,datetime
-from os.path import join, splitext, basename, exists, split
-
 def read_file (file,libname,dict_col, col_number=1):
     """
     Extract count from the count file 
@@ -64,72 +64,72 @@ def version_string ():
     return "merge_count.py " + __version__
 
 
-if __name__ == '__main__':
-    
-    parser = OptionParser(usage="Usage: %prog", description = "Merge files columns on first column, skip lines starting with #")
-    
-    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")
-    parser.add_option_group(igroup)
-    
-    ogroup = OptionGroup(parser, "Output files options","")
-    ogroup.add_option("-o", "--output", dest="output", help="the output count file")
-    parser.add_option_group(ogroup)
+
+
+parser = OptionParser(usage="Usage: %prog", description = "Merge files columns on first column, skip lines starting with #")
+
+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")
+parser.add_option_group(igroup)
+
+ogroup = OptionGroup(parser, "Output files options","")
+ogroup.add_option("-o", "--output", dest="output", help="the output count file")
+parser.add_option_group(ogroup)
+
+(options, args) = parser.parse_args()
+
+if options.files == None :
+    sys.stderr.write("Need files to merge\n")
+    parser.print_help()
+    sys.exit(1)
+
+if options.col_number < 1 :
+    sys.stderr.write("Column must be greater than 0 \n")
+    parser.print_help()
+    sys.exit(1)
     
-    (options, args) = parser.parse_args()
+if options.output == None:
+    sys.stderr.write("Output file is missing\n")
+    parser.print_help()
+    sys.exit(1)
 
-    if options.files == None :
-        sys.stderr.write("Need files to merge\n")
-        parser.print_help()
-        sys.exit(1)
+dict_col={}
+files = options.files.split(",")
+libs_name = []
+get_lib_name = True
+if options.names :
+    libs_name=options.names.split(",")
+    get_lib_name = False
+    if len(libs_name) != len(files):
+         sys.stderr.write("You must provide same number of files and names\n")
+         parser.print_help()
+         sys.exit(1)
 
-    if options.col_number < 1 :
-        sys.stderr.write("Column must be greater than 0 \n")
-        parser.print_help()
+current_libname=""
+for idx, line in enumerate(files):        
+    file = line.rstrip()
+    if exists(file) :
+        if get_lib_name : 
+            current_libname = splitext(basename(file))[0]
+            libs_name.append(current_libname)
+        else : 
+            current_libname = libs_name[idx]
+        read_file(file,current_libname,dict_col,options.col_number)
+    else :
+        sys.stderr.write("File : " + file + " doesn't exist")
         sys.exit(1)
-        
-    if options.output == None:
-        sys.stderr.write("Output file is missing\n")
-        parser.print_help()
-        sys.exit(1)
-    
-    dict_col={}
-    files = options.files.split(",")
-    libs_name = []
-    get_lib_name = True
-    if options.names :
-        libs_name=options.names.split(",")
-        get_lib_name = False
-        if len(libs_name) != len(files):
-             sys.stderr.write("You must provide same number of files and names\n")
-             parser.print_help()
-             sys.exit(1)
-
-    current_libname=""
-    for idx, line in enumerate(files):        
-        file = line.rstrip()
-        if exists(file) :
-            if get_lib_name : 
-                current_libname = splitext(basename(file))[0]
-                libs_name.append(current_libname)
-            else : 
-                current_libname = libs_name[idx]
-            read_file(file,current_libname,dict_col,options.col_number)
-        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")
-    # Pour tous les contigs : contruction de la ligne 
-    for contig_name in sorted(dict_col.keys()) :
-        line = []
-        line.append( contig_name )
-        # Pour toutes les contigs 
-        for lib in libs_name :
-            line.append( str(dict_col[contig_name][lib]) )
-        fout.write ( '\t'.join(line) +"\n")
-    fout.close
-    sys.exit(0)
+fout = open (options.output,"w")
+fout.write ( '#contig_name\t' + '\t'.join(libs_name) +"\n")
+# Pour tous les contigs : contruction de la ligne 
+for contig_name in sorted(dict_col.keys()) :
+    line = []
+    line.append( contig_name )
+    # Pour toutes les contigs 
+    for lib in libs_name :
+        line.append( str(dict_col[contig_name][lib]) )
+    fout.write ( '\t'.join(line) +"\n")
+fout.close
+sys.exit(0)
         
\ No newline at end of file