# BioPerl module for Bio::ClusterIO::unigene
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Andrew Macgregor <andrew at cbbc.murdoch.edu.au>
#
# Copyright Andrew Macgregor, Jo-Ann Stanton, David Green
# Molecular Embryology Group, Anatomy & Structural Biology, University of Otago
# http://meg.otago.ac.nz
#
# You may distribute this module under the same terms as perl itself
#
# _history
# April 17, 2002 - Initial implementation by Andrew Macgregor
# POD documentation - main docs before the code
=head1 NAME
Bio::ClusterIO::unigene - UniGene input stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the Bio::ClusterIO class.
=head1 DESCRIPTION
This object reads from Unigene *.data files downloaded from
ftp://ftp.ncbi.nih.gov/repository/UniGene/. It does not download and
decompress the file, you have to do that yourself.
=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:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHORS - Andrew Macgregor
Email: andrew at cbbc.murdoch.edu.au
=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::ClusterIO::unigene;
use strict;
use Bio::Cluster::UniGene;
use Bio::Cluster::ClusterFactory;
use base qw(Bio::ClusterIO);
my %line_is = (
ID => q/ID\s+(\w{2,3}\.\d+)/,
TITLE => q/TITLE\s+(\S.*)/,
GENE => q/GENE\s+(\S.*)/,
CYTOBAND => q/CYTOBAND\s+(\S.*)/,
MGI => q/MGI\s+(\S.*)/,
LOCUSLINK => q/LOCUSLINK\s+(\S.*)/,
HOMOL => q/HOMOL\s+(\S.*)/,
EXPRESS => q/EXPRESS\s+(\S.*)/,
RESTR_EXPR => q/RESTR_EXPR\s+(\S.*)/,
GNM_TERMINUS => q/GNM_TERMINUS\s+(\S.*)/,
CHROMOSOME => q/CHROMOSOME\s+(\S.*)/,
STS => q/STS\s+(\S.*)/,
TXMAP => q/TXMAP\s+(\S.*)/,
PROTSIM => q/PROTSIM\s+(\S.*)/,
SCOUNT => q/SCOUNT\s+(\S.*)/,
SEQUENCE => q/SEQUENCE\s+(\S.*)/,
ACC => q/ACC=(\w+)(\.\d+)?/,
NID => q/NID=\s*(\S.*)/,
PID => q/PID=\s*(\S.*)/,
CLONE => q/CLONE=\s*(\S.*)/,
END => q/END=\s*(\S.*)/,
LID => q/LID=\s*(\S.*)/,
MGC => q/MGC=\s*(\S.*)/,
SEQTYPE => q/SEQTYPE=\s*(\S.*)/,
TRACE => q/TRACE=\s*(\S.*)/,
PERIPHERAL => q/PERIPHERAL=\s*(\S.*)/,
DELIMITER => q{^//},
);
# we set the right factory here
sub _initialize {
my($self, @args) = @_;
$self->SUPER::_initialize(@args);
if(! $self->cluster_factory()) {
$self->cluster_factory(Bio::Cluster::ClusterFactory->new(
-type => 'Bio::Cluster::UniGene'));
}
}
=head2 next_cluster
Title : next_cluster
Usage : $unigene = $stream->next_cluster()
Function: returns the next unigene in the stream
Returns : Bio::Cluster::UniGene object
Args : NONE
=cut
sub next_cluster {
my( $self) = @_;
local $/ = "\n//";
return unless my $entry = $self->_readline;
# set up the variables we'll need
my (%unigene,@express,@locuslink,@chromosome,
@sts,@txmap,@protsim,@sequence);
my $UGobj;
# set up the regexes
# add whitespace parsing and precompile regexes
#foreach (values %line_is) {
# $_ =~ s/\s+/\\s+/g;
# print STDERR "Regex is $_\n";
# #$_ = qr/$_/x;
#}
#$line_is{'TITLE'} = qq/TITLE\\s+(\\S.+)/;
# run each line in an entry against the regexes
foreach my $line (split /\n/, $entry) {
#print STDERR "Wanting to match $line\n";
if ($line =~ /$line_is{ID}/gcx) {
$unigene{ID} = $1;
}
elsif ($line =~ /$line_is{TITLE}/gcx ) {
#print STDERR "MATCHED with [$1]\n";
$unigene{TITLE} = $1;
}
elsif ($line =~ /$line_is{GENE}/gcx) {
$unigene{GENE} = $1;
}
elsif ($line =~ /$line_is{CYTOBAND}/gcx) {
$unigene{CYTOBAND} = $1;
}
elsif ($line =~ /$line_is{MGI}/gcx) {
$unigene{MGI} = $1;
}
elsif ($line =~ /$line_is{LOCUSLINK}/gcx) {
@locuslink = split /;/, $1;
}
elsif ($line =~ /$line_is{HOMOL}/gcx) {
$unigene{HOMOL} = $1;
}
elsif ($line =~ /$line_is{EXPRESS}/gcx) {
my $express = $1;
# remove initial semicolon if present
$express =~ s/^;//;
@express = split /\s*;/, $express;
}
elsif ($line =~ /$line_is{RESTR_EXPR}/gcx) {
$unigene{RESTR_EXPR} = $1;
}
elsif ($line =~ /$line_is{GNM_TERMINUS}/gcx) {
$unigene{GNM_TERMINUS} = $1;
}
elsif ($line =~ /$line_is{CHROMOSOME}/gcx) {
push @chromosome, $1;
}
elsif ($line =~ /$line_is{TXMAP}/gcx) {
push @txmap, $1;
}
elsif ($line =~ /$line_is{STS}/gcx) {
push @sts, $1;
}
elsif ($line =~ /$line_is{PROTSIM}/gcx) {
push @protsim, $1;
}
elsif ($line =~ /$line_is{SCOUNT}/gcx) {
$unigene{SCOUNT} = $1;
}
elsif ($line =~ /$line_is{SEQUENCE}/gcx) {
# parse into each sequence line
my $seq = {};
# add unigene id to each seq
#$seq->{unigene_id} = $unigene{ID};
my @items = split(/;/, $1);
foreach (@items) {
if (/$line_is{ACC}/gcx) {
$seq->{acc} = $1;
# remove leading dot if version pattern matched
$seq->{version} = substr($2,1) if defined $2;
}
elsif (/$line_is{NID}/gcx) {
$seq->{nid} = $1;
}
elsif (/$line_is{PID}/gcx) {
$seq->{pid} = $1;
}
elsif (/$line_is{CLONE}/gcx) {
$seq->{clone} = $1;
}
elsif (/$line_is{END}/gcx) {
$seq->{end} = $1;
}
elsif (/$line_is{LID}/gcx) {
$seq->{lid} = $1;
}
elsif (/$line_is{MGC}/gcx) {
$seq->{mgc} = $1;
}
elsif (/$line_is{SEQTYPE}/gcx) {
$seq->{seqtype} = $1;
}
elsif (/$line_is{TRACE}/gcx) {
$seq->{trace} = $1;
}
elsif (/$line_is{PERIPHERAL}/gcx) {
$seq->{peripheral} = $1;
}
}
push @sequence, $seq;
}
elsif ($line =~ /$line_is{DELIMITER}/gcx) {
# at the end of the record, add data to the object
$UGobj = $self->cluster_factory->create_object(
-display_id => $unigene{ID},
-description => $unigene{TITLE},
-size => $unigene{SCOUNT},
-members => \@sequence);
$UGobj->gene($unigene{GENE}) if defined ($unigene{GENE});
$UGobj->cytoband($unigene{CYTOBAND}) if defined($unigene{CYTOBAND});
$UGobj->mgi($unigene{MGI}) if defined ($unigene{MGI});
$UGobj->locuslink(\@locuslink);
$UGobj->homol($unigene{HOMOL}) if defined ($unigene{HOMOL});
$UGobj->express(\@express);
$UGobj->restr_expr($unigene{RESTR_EXPR}) if defined ($unigene{RESTR_EXPR});
$UGobj->gnm_terminus($unigene{GNM_TERMINUS}) if defined ($unigene{GNM_TERMINUS});
$UGobj->chromosome(\@chromosome);
$UGobj->sts(\@sts);
$UGobj->txmap(\@txmap);
$UGobj->protsim(\@protsim);
}
}
return $UGobj;
}
1;