Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phyloconversion/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:
rev   line source
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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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 ##usage: ./pullgoodseqs.py <originalphytab> <bls2remove> <keep|discard> > outfile
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 #import modules
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 import sys, os, numpy, re
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 def read(filename):
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 f = open(filename)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 bad = open(sys.argv[2])
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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 badlines = bad.readlines()
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 badstripped = [line[:-1] for line in badlines]
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 str1 = '|'.join(badstripped)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 str2 = '('+str1[:-1]+')'
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 pattern = re.compile(str2)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 count=0
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 for line in lines:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 # line.strip()
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 match = pattern.findall(line)
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 if match and sys.argv[3] == 'keep':
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 print line,
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 if not match and sys.argv[3] == 'discard':
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 print line,
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 bad.close()
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 f.close()
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 def main():
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 read(sys.argv[1])
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 if __name__ == '__main__':
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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31 main()