scripts/tree/bp_nexus2nh.pl

   1 #!perl
   2
   3 =head1 NAME
   4
   5 bp_nexus2nh - convert nexus format trees (from PAUP* and MrBayes) to new hampshire
   6
   7 =head1 SYNOPSIS
   8
   9  bp_nexus2nh file.nexus > file.nh
  10
  11  # OR pipe in through STDIN
  12
  13  cat file.nexus | bp_nexus2nh > file.nh
  14
  15  # OR specify an output
  16
  17  bp_nexus2nh -o file.nh file.nexus
  18
  19 =head1 DESCRIPTION
  20
  21 Convert Nexus Tree files into Newick/New Hampshire format tree files.
  22
  23
  24 =cut
  25
  26 use strict;
  27 use warnings;
  28 use Bio::TreeIO;
  29 use Getopt::Long;
  30
  31 my $outfile;
  32
  33 GetOptions('o|out|outfile:s' => \$outfile);
  34
  35 my $in = Bio::TreeIO->new(-format => 'nexus', -fh => \*ARGV);
  36 my $out;
  37 if( $outfile ) {
  38     $out= Bio::TreeIO->new(-format => 'newick',
  39                            -file   => ">$outfile");
  40 } else {
  41     # write to STDOUT
  42     $out= Bio::TreeIO->new(-format => 'newick');
  43 }
  44
  45 while( my $t = $in->next_tree ) {
  46     $out->write_tree($t);
  47 }