Mercurial > repos > ucsb-phylogenetics > osiris_phylogenetics

annotate phylogenies/long_branch_finder.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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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: ./long_branch_finder.py <tabular treelist file> <number of stdevs as cut-off> > 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 lines = f.readlines()
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 for eachline in lines:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 line = eachline.split('\t')
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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12 gene = line[0]
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 d1 = {}
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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14 d1[gene] = line[1] #matches genename with its tree
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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15 treetips = re.findall('[a-zA-Z0-9]+(?:_[a-zA-Z0-9]+)?\w*:\d+\.\d+', line[1]) #should be more flexible in recognizing speciesnames in trees
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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16 # treetips = re.findall('[a-zA-Z0-9]+(?:_[a-zA-Z0-9]+)?:\d+\.\d+', line[1]) # makes a list of items like 'spname:bl'
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 #treetips = re.findall('[A-Z][a-z]+_[a-z]+:\d+\.\d+', line[1]) # makes a list of items like 'spname:bl'
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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18 d2 = {}
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 for i in treetips:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 spbl = i.split(':')
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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21 d2.update({spbl[1] : spbl[0]}) #creates link betwn taxon and its BL
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 tipbl = re.findall('\d+\.\d+', str(treetips))
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 std = numpy.std([float(i) for i in tipbl])
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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24 # numstd = 3*std
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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25 numstd = int(sys.argv[2])*std
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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26 for i in tipbl:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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27 if float(i) > float(numstd):
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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28 # print d2[str(i)] + '\t' + gene + '\t' + i
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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29 print d2[str(i)] + '\t' + gene
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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30 f.close()
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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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()