# HG changeset patch
# User davidvanzessen
# Date 1386000075 18000
# Node ID 591a8bc0af8e598d5d6d94badaa44e9de4b2aada
# Parent  30bbd9fe953cd7051dffcccd5422677b2781a96c
Uploaded

diff -r 30bbd9fe953c -r 591a8bc0af8e igblastmergems.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igblastmergems.py	Mon Dec 02 11:01:15 2013 -0500
@@ -0,0 +1,52 @@
+import sys
+# error
+def stop_err( msg ):
+	sys.stderr.write( "%s\n" % msg )
+	sys.exit()
+
+# main
+def main():
+    args = sys.argv[2:-2]
+
+    try:
+        o = open(sys.argv[-1], 'w')
+        i = open(args[1], 'r')
+        separator = "\t"
+        newline = "\n"
+        line = i.readline()
+        #write the header
+        o.write(line[:line.rfind(newline)] + separator + "Sample" + separator + "Replicate" + newline)
+        i.close()
+
+        current = 1
+        sampleID = args[0]
+        count = 1
+
+        while True:
+            print str(o)
+            f = open(args[current], 'r')
+            line = f.readline()
+            line = f.readline()
+            while line:
+                o.write(line[:line.rfind(newline)] + separator + sampleID + separator + str(count) + newline)
+                line = f.readline()
+            f.close()
+
+            if current >= (len(args) - 1):
+                break
+            if args[current + 1].find("/") is -1:
+                sampleID = args[current + 1]
+                current += 1
+                count = 1
+            else:
+                count += 1
+            current += 1
+        o.close()
+
+    except Exception, ex:
+        stop_err('Error running new_column.py\n' + str(ex))
+    sys.exit(0)
+
+if __name__ == "__main__":
+	print sys.argv
+	main()