bin/bp_tree2pag

   1 #!/usr/bin/perl
   2
   3 =head1 NAME
   4
   5 bp_tree2pag - convert Bio::TreeIO parseable format trees to pagel format
   6
   7 =head1 SYNOPSIS
   8
   9  bp_tree2pag -if nexus -i file.nexus > file.pag
  10
  11  # OR pipe in through STDIN, and use newick format instead
  12
  13  cat file.newick | bp_tree2pag -if newick > file.nh
  14
  15  # OR specify an output and input
  16
  17  bp_tree2pag -o file.pag -i file.newick
  18
  19 =head1 DESCRIPTION
  20
  21 Convert TreeIO parseable files into Pagel format tree files.  Be
  22 warned that pagel format only really supports a single tree per file
  23 so.  Also Pagel parsing is not yet available in bioperl.
  24
  25 =cut
  26
  27 use strict;
  28 use warnings;
  29 use Bio::TreeIO;
  30 use Getopt::Long;
  31 my ($iformat,$oformat) = ('newick', 'pag');
  32 my ($outfile,$infile);
  33 GetOptions(
  34            'if|informat:s'    => \$iformat,
  35            'of|outformat:s'   => \$oformat,
  36            'i|in:s'           => \$infile,
  37            'o|out:s'          => \$outfile,
  38            'h|help'           => sub { exec('perldoc', $0);
  39                                        exit(0); },
  40            );
  41 my $in;
  42 if( ! $infile ) {
  43     $in = Bio::TreeIO->new(-format => $iformat,
  44                            -fh     => \*ARGV);
  45 } else {
  46     $in = Bio::TreeIO->new(-format => $iformat,
  47                            -file   => $infile);
  48 }
  49
  50 my $out;
  51 if( $outfile) {
  52     $out = Bio::TreeIO->new(-format => $oformat,
  53                             -file   => ">$outfile");
  54 } else {
  55     $out = Bio::TreeIO->new(-format => $oformat); #print to STDOUT instead
  56 }
  57
  58 while( my $t = $in->next_tree ) {
  59     $out->write_tree($t);
  60 }