/usr/share/perl5/Bio/AlignIO/selex.pm is in libbio-perl-perl 1.6.924-3.
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# BioPerl module for Bio::AlignIO::selex
# based on the Bio::SeqIO::selex 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
=head1 NAME
Bio::AlignIO::selex - selex sequence input/output stream
=head1 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 => 'selex',
-file => 't/data/testaln.selex');
while( my $aln = $in->next_aln ) {
}
=head1 DESCRIPTION
This object can transform L<Bio::Align::AlignI> objects to and from selex flat
file databases.
=head1 FEEDBACK
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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://github.com/bioperl/bioperl-live/issues
=head1 AUTHORS - Peter Schattner
Email: schattner@alum.mit.edu
=head1 CONTRIBUTORS
Jason Stajich, jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::AlignIO::selex;
use strict;
use base qw(Bio::AlignIO);
=head2 next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream. Tries to read *all* selex
It reads all non whitespace characters in the alignment
area. For selexs with weird gaps (eg ~~~) map them by using
$al->map_chars('~','-')
Returns : L<Bio::Align::AlignI> object
Args : NONE
=cut
sub next_aln {
my $self = shift;
my $entry;
my ($start,$end,%align,$name,$seqname,%hash,@c2name, %accession,%desc);
my $aln = Bio::SimpleAlign->new(-source => 'selex');
# in selex format, every non-blank line that does not start
# with '#=' is an alignment segment; the '#=' lines are mark up lines.
# Of particular interest are the '#=GF <name/st-ed> AC <accession>'
# lines, which give accession numbers for each segment
while( $entry = $self->_readline) {
if( $entry =~ /^\#=GS\s+(\S+)\s+AC\s+(\S+)/ ) {
$accession{ $1 } = $2;
next;
} elsif( $entry =~ /^\#=GS\s+(\S+)\s+DE\s+(.+)\s*$/ ) {
$desc{$1} .= $2;
} elsif ( $entry =~ /^([^\#]\S+)\s+([A-Za-z\.\-\*]+)\s*/ ) {
my ($name,$seq) = ($1,$2);
if( ! defined $align{$name} ) {
push @c2name, $name;
}
$align{$name} .= $seq;
}
}
# ok... now we can make the sequences
foreach my $name ( @c2name ) {
if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
$seqname = $1;
$start = $2;
$end = $3;
} else {
$seqname=$name;
$start = 1;
$end = length($align{$name});
}
my $seq = Bio::LocatableSeq->new
('-seq' => $align{$name},
'-display_id' => $seqname,
'-start' => $start,
'-end' => $end,
'-description' => $desc{$name},
'-accession_number' => $accession{$name},
'-alphabet' => $self->alphabet,
);
$aln->add_seq($seq);
}
return $aln if $aln->num_sequences;
return;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in selex format
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
=cut
sub write_aln {
my ($self,@aln) = @_;
my ($namestr,$seq,$add);
my ($maxn);
foreach my $aln (@aln) {
$maxn = $aln->maxdisplayname_length();
foreach $seq ( $aln->each_seq() ) {
$namestr = $aln->displayname($seq->get_nse());
$add = $maxn - length($namestr) + 2;
$namestr .= " " x $add;
$self->_print (sprintf("%s %s\n",$namestr,$seq->seq())) or return;
}
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
1;
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