Fields, Christopher J | 11 Jan 06:04 2013

Re: Error when using Bio::AlignIO on stockholm file from Pfam

I haven't used the '/dev/stdin' file like this, I typically do:

> my $in = Bio::AlignIO->new(
>  -format => 'stockholm',
>  -fh   => \*STDIN
> );

but if it works…

That does look like a bug in the parser.  Would you know the Pfam alignmet accessions that triggered it, or
maybe ones just prior to the fail?

chris

On Jan 3, 2013, at 4:41 PM, Peng Yu <pengyu.ut <at> gmail.com> wrote:

> 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
> -------------------------------------
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Gmane