————#
# BioPerl module for FAST::Bio::Tools::Genomewise
#
# Copyright Jason Stajich <jason-at-bioperl.org>
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
FAST::Bio::Tools::Genomewise - Results of one Genomewise run
=head1 SYNOPSIS
use FAST::Bio::Tools::Genomewise;
my $gw = FAST::Bio::Tools::Genomewise(-file=>"genomewise.out");
while (my $gene = $gw->next_prediction){
my @transcripts = $gene->transcripts;
foreach my $t(@transcripts){
my @exons = $t->exons;
foreach my $e(@exons){
print $e->start." ".$e->end."\n";
}
}
}
=head1 DESCRIPTION
This is the parser for the output of Genewise. It takes either a file
handle or a file name and returns a
FAST::Bio::SeqFeature::Gene::GeneStructure object. You will need to specify
the proper target sequence id on the object with the
$feature-E<gt>seq_id($seqid).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=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:
=head1 AUTHOR - Fugu Team, Jason Stajich
Email: fugui-at-worf.fugu-sg.org
jason-at-bioperl-dot-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
FAST::Bio::Tools::Genomewise;
use
strict;
$Srctag
=
'genomewise'
;
=head2 new
Title : new
Usage : $obj->new(-file=>"genewise.out");
$obj->new(-fh=>\*GW);
Function: Constructor for genomewise wrapper. Takes either a file or filehandle
Example :
Returns : L<FAST::Bio::Tools::Genomewise>
=cut
sub
new {
my
(
$class
,
@args
) =
@_
;
my
$self
=
$class
->SUPER::new(
@args
);
return
$self
;
}
=head2 _get_strand
Title : _get_strand
Usage : $obj->_get_strand
Function: takes start and end values, swap them if start>end and returns end
Example :
Returns :$start,$end,$strand
=cut
=head2 score
Title : score
Usage : $obj->score
Function: get/set for score info
Example :
Returns : a score value
=cut
=head2 _prot_id
Title : _prot_id
Usage : $obj->_prot_id
Function: get/set for protein id
Example :
Returns :a protein id
=cut
=head2 _target_id
Title : _target_id
Usage : $obj->_target_id
Function: get/set for genomic sequence id
Example :
Returns :a target id
=cut
=head2 next_prediction
Title : next_prediction
Usage : while($gene = $genewise->next_prediction()) {
# do something
}
Function: Returns the gene structure prediction of the Genomewise result
file. Call this method repeatedly until FALSE is returned.
Example :
Returns : a FAST::Bio::SeqFeature::Gene::GeneStructure object
Args :
=cut
sub
next_prediction {
my
(
$self
) =
@_
;
my
$genes
;
while
(
$_
=
$self
->_readline) {
$self
->debug(
$_
);
last
if
m{^//};
if
( /^Gene\s+\d+\s*$/ ) {
$genes
= FAST::Bio::SeqFeature::Gene::GeneStructure->new
(
-source
=>
$Srctag
,
-seq_id
=>
$self
->_target_id,
# if this had been specified
);
$_
=
$self
->_readline;
$self
->debug(
$_
);
unless
( /^Gene\s+(\d+)\s+(\d+)\s*$/ ) {
$self
->
warn
(
"Unparseable genomewise output"
);
last
;
}
my
$transcript
= FAST::Bio::SeqFeature::Gene::Transcript->new
(
-source
=>
$Srctag
,
-seq_id
=>
$self
->_target_id,
# if this had been specified
-start
=> $1,
-end
=> $2,
);
my
$nbr
= 1;
while
(
$_
=
$self
->_readline ) {
$self
->debug(
$_
);
unless
( m/^\s+Exon\s+(\d+)\s+(\d+)\s+phase\s+(\d+)/ ){
$self
->_pushback(
$_
);
last
;
}
my
(
$e_start
,
$e_end
,
$phase
,
$e_strand
) = ($1,$2,$3);
(
$e_start
,
$e_end
,
$e_strand
) =
$self
->_get_strand(
$e_start
,
$e_end
);
$transcript
->strand(
$e_strand
)
unless
$transcript
->strand != 0;
my
$exon
= FAST::Bio::SeqFeature::Gene::Exon->new
(
-seq_id
=>
$self
->_target_id,
-source
=>
$Srctag
,
-start
=>
$e_start
,
-end
=>
$e_end
,
-frame
=>
$phase
,
-strand
=>
$e_strand
);
$exon
->add_tag_value(
"Exon"
,
$nbr
++);
$exon
->add_tag_value(
'phase'
,
$phase
);
$transcript
->add_exon(
$exon
);
}
$genes
->add_transcript(
$transcript
);
last
;
# only process a single gene at a time
}
}
return
$genes
;
}
1;