NAME

Bio::AlignIO::stockholm - stockholm sequence input/output stream

SYNOPSIS

# Do not use this module directly.  Use it via the L<Bio::AlignIO> class.

use Bio::AlignIO;
use strict;

my $in = Bio::AlignIO->new(-format => 'stockholm',
                           -file   => 't/data/testaln.stockholm');
while( my $aln = $in->next_aln ) {

}

DESCRIPTION

This object can transform Bio::Align::AlignI objects to and from stockholm flat file databases.

Note that many Stockholm sequence files contain additional sequence-based and alignment-based annotation

GF Lines (alignment feature/annotation):
#=GF <featurename> <Generic per-file annotation, free text>
Placed above the alignment

GC Lines (Alignment consensus)
#=GC <featurename> <Generic per-column annotation, exactly 1
     character per column>
Placed below the alignment

GS Lines (Sequence annotations)
#=GS <seqname> <featurename> <Generic per-sequence annotation, free
     text>

GR Lines (Sequence meta data)
#=GR <seqname> <featurename> <Generic per-sequence AND per-column
     mark up, exactly 1 character per column>

This module is currently being refactored to incorporate Meta data for sequences and alignments. Annotations are also now added for alignments.

Note that sequence names in the alignment are cut off at

FEEDBACK

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

http://bugzilla.open-bio.org/

AUTHORS - Peter Schattner, Chris Fields

Email: schattner@alum.mit.edu, cjfields-at-uiuc-dot-edu

CONTRIBUTORS

Chris Fields, cjfields-at-uiuc-dot-edu Andreas Kahari, ak-at-ebi.ac.uk Jason Stajich, jason-at-bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_aln

Title   : next_aln
Usage   : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
Returns : L<Bio::Align::AlignI> object
Args    : NONE

write_aln

Title   : write_aln
Usage   : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in stockholm format
Returns : 1 for success and 0 for error
Args    : L<Bio::Align::AlignI> object