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annotate phylostatistics/PD.pl @ 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
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl -w
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2
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3 use strict;
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4
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5 #use FindBin;
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6 #use lib "$FindBin::Bin/lib";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 use Bio::TreeIO;
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8 use Bio::Tree::Tree;
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9
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10 ###this script will find the phylogenetic distance between two species
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11 #input is a tree, output filename, and table with pairwise distances
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12 #usage:
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13 #PD.pl <pairsTable> <treefile> <outfile> <yes|no>
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14 # parse in newick/new hampshire format
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15 my @species1;
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16 my @species2;
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17
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18
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19 my $half=$ARGV[3];
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20 my $divtimebool;
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21 if($half eq 'yes'){
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22 $divtimebool=1;
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23 }elsif($half eq 'no'){
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24 $divtimebool=0;
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25 }else{
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26 die "Argument must contain yes or no for divergence times\n";
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27 }
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28 my $outfile = $ARGV[2];
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29 open(OUT, ">$outfile") or die("Couldn't open output file $ARGV[2]\n");
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30
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31
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32 my $pairsfile = $ARGV[0];
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33 open(PAIRS, "$pairsfile") or die("Couldn't open input file $ARGV[0]\n");
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34 while (<PAIRS>) {
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35 chomp;
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36 my $sp1;
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37 my $sp2;
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38 ($sp1, $sp2) = split("\t");
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39 push(@species1, $sp1);
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40 push(@species2, $sp2);
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41 }
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42
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43 my $treefile = $ARGV[1];
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44
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45 for(my $i=0; $i < @species1; $i++){
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46 print OUT $species1[$i]."\t".$species2[$i];
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47 open(TREE, "$treefile") or die("Couldn't open output file $ARGV[1]\n");
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48
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49 my $treeio = new Bio::TreeIO('-format' => 'newick',
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50 '-file' => $treefile);
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51
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52 while(my $tree = $treeio->next_tree){;
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53 my $node1 = $tree->find_node(-id => $species1[$i]);
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54 my $node2 = $tree->find_node(-id => $species2[$i]);
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55 my $distances = $tree->distance(-nodes => [$node1,$node2]);
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56
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57 #ADD OPTION FOR DIVIDING BY 2 FOR DIVERGENCE TIMES
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58 if($divtimebool==1){
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59 $distances = $distances/2 ;
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60 }
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61 print OUT "\t".$distances;
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62 }
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63 print OUT "\n";
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64 close(TREE);
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65 }
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66
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67 close(PAIRS);
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68 close(OUT);