diff mergeCols.py @ 0:11de536c87b1 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/merge_cols commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mergeCols.py	Mon Nov 09 11:45:18 2015 -0500
@@ -0,0 +1,37 @@
+import sys, re
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+def __main__():
+    try:
+        infile =  open ( sys.argv[1], 'r')
+        outfile = open ( sys.argv[2], 'w')
+    except:
+        stop_err( 'Cannot open or create a file\n' )
+        
+    if len( sys.argv ) < 4:
+        stop_err( 'No columns to merge' )
+    else:
+        cols = sys.argv[3:]        
+
+    skipped_lines = 0
+
+    for line in infile:
+        line = line.rstrip( '\r\n' )
+        if line and not line.startswith( '#' ):
+            fields = line.split( '\t' )
+            line += '\t'
+            for col in cols:
+                try:
+                    line += fields[ int( col ) -1 ]
+                except:
+                    skipped_lines += 1
+                    
+            print >>outfile, line
+            
+    if skipped_lines > 0:
+        print 'Skipped %d invalid lines' % skipped_lines
+            
+if __name__ == "__main__" : __main__()
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