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Gmane
From: Peng Yu <pengyu.ut <at> gmail.com>
Subject: Error when using Bio::AlignIO on stockholm file from Pfam
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Thursday 3rd January 2013 22:41:37 UTC (over 3 years ago)
Hi,

I tried the following code on the Pfam stockholm file (downloaded at
ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.full.gz).
But it gives me the following error. Is it a bug in bioperl or it is
an error in the Pfam-A.full.gz file?

~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main.pl
#!/usr/bin/env perl

use strict;
use warnings;

#use FindBin;
#use lib "$FindBin::Bin/.";

use Bio::AlignIO;
use Data::Dumper;

my $in = Bio::AlignIO->new(
  -format => 'stockholm',
  -file   => '/dev/stdin'
);

while(my $aln=$in->next_aln) {
  print $aln->accession, "\n";
}

~/linux/bin/xplat/src/stk/stk2acc/perl$ cat main_full.sh
#!/usr/bin/env bash

zcat ~/db/Pfam-A.full.gz | ./main.pl

~/linux/bin/xplat/src/stk/stk2acc/perl$ ./main_full.sh

...

------------- EXCEPTION -------------
MSG: '1985D' is not an integer.

STACK Bio::Range::end /Users/py/Library/ActivePerl-5.14/lib/Bio/
Range.pm:227
STACK Bio::Annotation::Target::new /Users/py/Library/ActivePerl-5.14/
lib/Bio/Annotation/Target.pm:81
STACK Bio::AlignIO::Handler::GenericAlignHandler::_stockholm_target /
Users/py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
GenericAlignHandler.pm:293
STACK Bio::AlignIO::Handler::GenericAlignHandler::data_handler /Users/
py/Library/ActivePerl-5.14/lib/Bio/AlignIO/Handler/
GenericAlignHandler.pm:73
STACK Bio::AlignIO::stockholm::next_aln /Users/py/Library/
ActivePerl-5.14/lib/Bio/AlignIO/stockholm.pm:470
STACK toplevel ./main.pl:17
-------------------------------------
 
CD: 12ms