--- a/igblastmerge.py	Mon Dec 02 11:01:15 2013 -0500
+++ b/igblastmerge.py	Mon Dec 02 11:01:49 2013 -0500
@@ -1,4 +1,3 @@
-import argparse
 import sys
 # error
 def stop_err( msg ):
@@ -7,35 +6,46 @@
 
 # main
 def main():
-	parser = argparse.ArgumentParser() #docs.python.org/dev/library/argparse.html
-	parser.add_argument("--input", help="Input file(s)", nargs="+")
-	parser.add_argument("--id", help="Input file(s) id's", nargs="+")
-	parser.add_argument("--output", help="Output file")
-	
-	args = parser.parse_args()
-	try:
-		o = open(args.output, 'w')
-		i = open(args.input[-1], 'r')
-		separator = "\t"
-		newline = "\n"
-		header = "Sample"
-		line = i.readline()
-		o.write(line[:line.rfind(newline)] + separator + header + newline) #write the header
-		i.close()
-		
-		for cf,i in zip(args.input,args.id):
-			f = open(cf, 'r')
-			line = f.readline()
-			line = f.readline() #skip header
-			while line:
-				o.write(line[:line.rfind(newline)] + separator + i + newline)
-				line = f.readline()
-			f.close()
-		o.close()
-    
-	except Exception, ex:
-		stop_err('Error running new_column.py\n' + str(ex))
-	sys.exit(0)
+    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