scripts/run_neighbor.PLS

   1 #!/usr/bin/perl -w
   2 use strict;
   3
   4 =head1 NAME
   5
   6 run_neighbor - run Phylip's 'neighbor' program through Bioperl
   7
   8 =head1 SYNOPSIS
   9
  10 run_neighbor [-i inputfile] [-o outfilename]
  11
  12 =head1 DESCRIPTION
  13
  14 Provide an matrix file to run neighbor on.  File should be named of
  15 the forma file.matrix or file.protdist (the ending doesn't matter, but
  16 the program expects a file in the form of (\S+)\.(\S+).
  17
  18 This will run the application 'neighbor' to build a
  19 Neighbor-Joining tree from a protein distance matrix.
  20
  21 =head1 AUTHOR
  22
  23 Jason Stajich, jason-AT-open-bio-DOT-org
  24
  25 =cut
  26
  27 use Bio::TreeIO;
  28 use Bio::Tools::Run::Phylo::Phylip::Neighbor;
  29 use Getopt::Long;
  30
  31 my @params = ('type'=>'NJ', 'quiet' => 1);
  32
  33 my $matrixfile;
  34 my $out;
  35 GetOptions(
  36            'i|input:s' => \$matrixfile,
  37            'o|out:s'   => \$out,
  38            'h|help'    => sub { exec('perldoc',$0); exit(0) }
  39            );
  40 ($matrixfile) ||= shift @ARGV;
  41
  42 my ($stem,$ext) = ($matrixfile =~ /(\S+)\.(\S+)$/) ;
  43 $stem ||= $matrixfile;
  44
  45 my $outfh;
  46 if( $out ) {
  47     open($outfh, ">$out") || die($!);
  48 } else {
  49     open($outfh, ">$stem.tree") || die($!);
  50 }
  51
  52 my $tree_factory = Bio::Tools::Run::Phylo::Phylip::Neighbor->new(@params);
  53 my (@trees) = $tree_factory->create_tree($matrixfile);
  54
  55 my $outtree = new Bio::TreeIO(-fh => $outfh);
  56 foreach my $tree ( @trees ){
  57     $outtree->write_tree($tree);
  58 }