[Bioperl-guts-l] [Bug 1822] New: nhx.pm does not print bootstrap values

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Fri Jul 1 18:23:21 EDT 2005


http://bugzilla.open-bio.org/show_bug.cgi?id=1822

           Summary: nhx.pm does not print bootstrap values
           Product: Bioperl
           Version: main-trunk
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: critical
          Priority: P2
         Component: Unclassified
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: rfsouza at cecm.usp.br


I been trying to reformat some phylogenies built by the Phyml program to
the nhx format, in order to print them through ATV, but, for some reason,
the nhx.pm module doesn't print the bootstrap values.

Those values are loaded using newick.pm and get printed out through
nexus.pm, but nhx.pm seems to loose them. I'm using bioperl-live from
CVS (downloaded 20050523). Is this a known bug? See code below.

It seems that Bio::TreeIO::nhx.pm is not holding ANY tag values, not only the
bootstrap ones, but I'm not sure about it... ???

Robson

#!/usr/bin/perl -w

use Bio::TreeIO;
use Getopt::Long;
use strict;

my $usage = 0;
my $outfile = undef;
my $infmt = 'newick';
my $outfmt = 'nhx';
my $bootstyle = '';
GetOptions("infmt|i=s" => \$infmt,
           "outfmt|o=s" => \$outfmt,
           "bootstyle|b=s" => \$bootstyle,
           "outfile|f=s" => \$outfile,
           "usage|help|h" => \$usage)
    || die "Error parsing command line arguments";
usage() if ($usage || scalar(@ARGV) == 0);

# Storing input file command line arguments
my %inargs = ('-file'=>$ARGV[0], '-format'=>$infmt);
$inargs{'-bootstrap_style'} = $bootstyle if (defined $bootstyle);

# Storing input file command line arguments
my %outargs = ('-format'=>$outfmt);
if (defined $outfile) {
    $outargs{'-file'} = ">$outfile";
} else {
    $outargs{'-fh'} = \*STDOUT;
}

# Building data streams
my $in  = Bio::TreeIO->new(%inargs);
my $out = Bio::TreeIO->new(%outargs);
while (my $t = $in->next_tree) {
    $out->write_tree($t);
}

exit 0;

sub usage {
    die "Usage: $0 [options] <file1> <file2>...
Available options:
 --infmt|-i    <string> : input file format (default: newick)
 --outfmt|-o   <string> : output file format (default: nhx)
 --bootstyle|b <string> : input bootstrap values format
 --outfile|-f  <file>   : output file name (default: stdout)
 --usage|--help|-h      : print this message
";
}



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