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

BioPerl documentation

Contained in the BioPerl distribution.

Index

NAME
SYNOPSIS
DESCRIPTION
FEEDBACK
- Support
- Reporting Bugs
AUTHORS - Peter Schattner
APPENDIX
- next_aln
- write_aln

Code Index:

package Bio::AlignIO::prodom
- next_aln
- write_aln
EOF

NAME

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

SYNOPSIS

Do not use this module directly. Use it via the Bio::AlignIO class.

DESCRIPTION

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

FEEDBACK

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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:

  https://redmine.open-bio.org/projects/bioperl/

AUTHORS - Peter Schattner

Email: schattner@alum.mit.edu

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 prodom format  ###Not yet implemented!###
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object

BioPerl documentation

Contained in the BioPerl distribution.

#
# BioPerl module for Bio::AlignIO::prodom

#   based on the Bio::SeqIO::prodom module
#       by Ewan Birney <birney@ebi.ac.uk>
#       and Lincoln Stein  <lstein@cshl.org>
#
#       and the SimpleAlign.pm module of Ewan Birney
#
# Copyright Peter Schattner
#
# You may distribute this module under the same terms as perl itself
# _history
# September 5, 2000
# POD documentation - main docs before the code

# Let the code begin...

package Bio::AlignIO::prodom;
use strict;


use base qw(Bio::AlignIO);

sub next_aln {
    my $self = shift;
    my $entry;
    my ($acc, $fake_id, $start, $end, $seq, $add, %names);

    my $aln =  Bio::SimpleAlign->new(-source => 'prodom');

    while( $entry = $self->_readline) {

       if ($entry =~ /^AC\s+(\S+)\s*$/) {         #ps 9/12/00
	   $aln->id( $1 );
       }
       elsif ($entry =~ /^AL\s+(\S+)\|(\S+)\s+(\d+)\s+(\d+)\s+\S+\s+(\S+)\s*$/){    #ps 9/12/00
	   $acc=$1;
	   $fake_id=$2;  # Accessions have _species appended
	   $start=$3;
	   $end=$4;
	   $seq=$5;

	   $names{'fake_id'} = $fake_id;

	   $add = Bio::LocatableSeq->new('-seq'      => $seq,
					 '-id'       => $acc,
					 '-start'    => $start,
					 '-end'      => $end,
					 '-alphabet' => $self->alphabet,
			       );

	   $aln->add_seq($add);
       }
       elsif ($entry =~ /^CO/) {
	   # the consensus line marks the end of the alignment part of the entry
	   last;
       }
	}
	
   return $aln if $aln->num_sequences;
   return;
}

sub write_aln {
    my ($self,@aln) = @_;
    $self->throw_not_implemented();
}

1;