Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

comparison phylogenies/prune_phytab_using_list.py @ 0:5b9a38ec4a39 draft default tip

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author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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-1:000000000000 0:5b9a38ec4a39
1 #!/usr/bin/python -tt
2
3 ##usage: ./prune_phytab_using_list.py <originalphytab> <bls2remove> <keep|discard> > outfile
4
5 #import modules
6 import sys, os, numpy, re
7
8 def read(filename):
9 f = open(filename)
10 lines = f.readlines()
11 # for case where list is an empty file (here, under 20 bytes)
12 if os.lstat(sys.argv[2]).st_size < 20:
13 for line in lines:
14 print line,
15 else:
16 bad = open(sys.argv[2])
17 badlines = bad.readlines()
18 badstripped = [line[:-1] for line in badlines]
19 str1 = '|'.join(badstripped)
20 str2 = '('+str1[:-1]+')'
21 pattern = re.compile(str2)
22 count=0
23 for line in lines:
24 match = pattern.findall(line)
25 if match and sys.argv[3] == 'keep':
26 print line,
27 if not match and sys.argv[3] == 'discard':
28 print line,
29 bad.close()
30 f.close()
31
32 def main():
33 read(sys.argv[1])
34
35 if __name__ == '__main__':
36 main()
37
38