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annotate phylogenies/makeNJst.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
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl
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2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 #This script generates an R script to call NJst
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4 #input is a table with treename<tab>newick tree
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5 use strict;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 use Bio::TreeIO;
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7
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8 my $filename = $ARGV[0];
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9 my $outfile = $ARGV[1];
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10 open FILE, $filename or die $!;
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11
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12
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 my @splitline;
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14
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15 print "require(phybase);\n";
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16 print "genetrees<-c(";
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17 my $counter=0;
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18 my $tree;
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19 while (<FILE>) {
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20 chomp;
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21 #get a line from the data file
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22 my $currentinput = "$_";
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23 @splitline = split(/\t/);
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24 my $treename= $splitline[0];
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25 $tree = $splitline[1];
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26 unless($counter==0){
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27 print ", ";
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28 }
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29 $counter++;
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30 print "'$tree'";
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31 }
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32 print ")\n"; #close genetree vector
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33 print "taxaname<-c(";
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34 my $spnum = tree2spList($tree);
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35 print ")\nspname<-taxaname\n";
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36 print "species.structure<-matrix(0,$spnum,$spnum)\n";
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37 print "diag(species.structure)<-1\n";
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38 print "\n";
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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39 print "result<-NJst(genetrees,taxaname,spname,species.structure)\n";
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40 print "write(result, file='$outfile')\n";
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41 close FILE;
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42
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43
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44
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45
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46
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47 #This script requires phybase R package
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48 #NJst is a function used as follows
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49 # genetrees<-c("(A:0.004,(B:0.003,(C:0.002,(D:0.001,E:0.001)
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50 # :0.001):0.001):0.001);","(A:0.004,(B:0.003,(E:0.002,(D:0.001,C:0.001):0.001):0.001):0.001);","(A:0.004,(B:0.003,(C:0.002,(D:0.001,E:0.001):0.001):0.001):0.001);")
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51 # taxaname<-c("A","B","C","D","E")
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52 # spname<-taxaname
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53 # species.structure<-matrix(0, 5, 5)
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54 # diag(species.structure)<-1
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55 #
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56 # NJst(genetrees,taxaname, spname, species.structure)
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57
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58
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59
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60 sub tree2spList {
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61 my $treefile=shift;
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62
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63 my ($charactername, $characterstate);
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64 my ($call, $sp_id, $char_id);
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65
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66 #Open treefile and get taxon names from tree
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67 my $stringfh;
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68 open($stringfh, "<", \$treefile);
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69
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70 my $input = Bio::TreeIO->new(-format => 'newick', -fh => $stringfh);
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71 my $tree = $input->next_tree;
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72
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73 my @taxa = $tree->get_leaf_nodes;
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74 my @names = map { $_->id } @taxa;
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75
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76 my $count=0;
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77 foreach(@names){
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78 my $treespecies = $_;
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79 $treespecies =~ s/^\s+|\s+$//g ; #Trim leading and trailing whitespace
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80 unless($count==0){
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81 print ",";
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82 }
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83 print "'$treespecies'";
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84 $count++
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85 }
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86 return $count;
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87 } #end of tree2spList subroutine