Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

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

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