Mercurial > repos > davidvanzessen > combined_immune_repertoire_imgt

comparison igblastmerge.py @ 1:d2b3bcabb478 draft

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Uploaded
author davidvanzessen
date Mon, 09 Dec 2013 06:08:52 -0500
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children 8ba0fd5b03a1
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0:e71c59b72669 1:d2b3bcabb478
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 print args
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 f = open(args[current], 'r')
27 line = f.readline()
28 line = f.readline()
29 while line:
30 o.write(line[:line.rfind(newline)] + separator + sampleID + separator + str(count) + newline)
31 line = f.readline()
32 f.close()
33
34 if current >= (len(args) - 1):
35 break
36 if args[current + 1].find("/") is -1:
37 sampleID = args[current + 1]
38 current += 1
39 count = 1
40 else:
41 count += 1
42 current += 1
43 o.close()
44
45 except Exception, ex:
46 stop_err('Error running new_column.py\n' + str(ex))
47 sys.exit(0)
48
49 if __name__ == "__main__":
50 print sys.argv
51 main()