Mercurial > repos > davidvanzessen > experimental_design_igg
comparison igblastmerge.py @ 0:03dbb4601b15 draft
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| author | davidvanzessen |
|---|---|
| date | Thu, 23 Jan 2014 08:14:08 -0500 |
| parents | |
| children | 07a23652bc2a |
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| -1:000000000000 | 0:03dbb4601b15 |
|---|---|
| 1 import sys | |
| 2 # error | |
| 3 def stop_err( msg ): | |
| 4 sys.stderr.write( "%s\n" % msg ) | |
| 5 sys.exit() | |
| 6 | |
| 7 # main | |
| 8 def main(): | |
| 9 args = sys.argv[1:-2] | |
| 10 | |
| 11 try: | |
| 12 o = open(sys.argv[-1], 'w') | |
| 13 i = open(args[1], 'r') | |
| 14 separator = "\t" | |
| 15 newline = "\n" | |
| 16 line = i.readline() | |
| 17 #write the header | |
| 18 o.write(line[:line.rfind(newline)] + separator + "Sample" + separator + "Replicate" + newline) | |
| 19 i.close() | |
| 20 | |
| 21 current = 1 | |
| 22 sampleID = args[0] | |
| 23 count = 1 | |
| 24 | |
| 25 while True: | |
| 26 print str(o) | |
| 27 f = open(args[current], 'r') | |
| 28 line = f.readline() | |
| 29 line = f.readline() | |
| 30 while line: | |
| 31 o.write(line[:line.rfind(newline)] + separator + sampleID + separator + str(count) + newline) | |
| 32 line = f.readline() | |
| 33 f.close() | |
| 34 | |
| 35 if current >= (len(args) - 1): | |
| 36 break | |
| 37 if args[current + 1].find("/") is -1: | |
| 38 sampleID = args[current + 1] | |
| 39 current += 1 | |
| 40 count = 1 | |
| 41 else: | |
| 42 count += 1 | |
| 43 current += 1 | |
| 44 o.close() | |
| 45 | |
| 46 except Exception, ex: | |
| 47 stop_err('Error running new_column.py\n' + str(ex)) | |
| 48 sys.exit(0) | |
| 49 | |
| 50 if __name__ == "__main__": | |
| 51 print sys.argv | |
| 52 main() |