# HG changeset patch
# User davidvanzessen
# Date 1384353997 18000
# Node ID 83cb18fb0a87f006fe6727cfb72df75c18947fb7
# Parent  14e80e5c33534e83dd5863ff4d2d6c30a7a796d8
Uploaded

diff -r 14e80e5c3353 -r 83cb18fb0a87 imgtconvert.py
--- a/imgtconvert.py	Wed Nov 13 09:36:48 2013 -0500
+++ b/imgtconvert.py	Wed Nov 13 09:46:37 2013 -0500
@@ -3,6 +3,9 @@
 import argparse
 import os
 
+def stop_err( msg, ret=1 ):
+    sys.stderr.write( msg )
+    sys.exit( ret )
 
 #docs.python.org/dev/library/argparse.html
 parser = argparse.ArgumentParser()
@@ -19,17 +22,18 @@
 added_sequence_columns = [u'FR1-IMGT', u'FR2-IMGT', u'FR3-IMGT', u'CDR3-IMGT', u'JUNCTION', u'J-REGION', u'FR4-IMGT']
 added_junction_columns = [u"P3'V-nt nb", u'N1-REGION-nt nb', u"P5'D-nt nb", u"P3'D-nt nb", u'N2-REGION-nt nb', u"P5'J-nt nb", u"3'V-REGION trimmed-nt nb", u"5'D-REGION trimmed-nt nb", u"3'D-REGION trimmed-nt nb", u"5'J-REGION trimmed-nt nb"]
 
+inputFolder = args.input
 
-dirContents = os.listdir(args.input)
+dirContents = os.listdir(inputFolder)
 if len(dirContents) == 1:
-    if os.path.isdir(dirContents[0]):
-        dirContents = os.listdir(dirContents[0])
-files = sorted([os.path.join(args.input, f) for f in dirContents])
-
-print files
+    inputFolder = os.path.join(inputFolder, dirContents[0])
+    if os.path.isdir(inputFolder):
+        print "is dir"
+        dirContents = os.listdir(inputFolder)
+files = sorted([os.path.join(inputFolder, f) for f in dirContents])
 
 if len(files) % 3 is not 0:
-    print "Files in zip not a multiple of 3, it should contain the all the 1_, 5_ and 6_ files for a sample"
+    stop_err("Files in zip not a multiple of 3, it should contain the all the 1_, 5_ and 6_ files for a sample")
     import sys
     sys.exit()