Bio::ClusterIO unigene
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Toolbar
WebCvs
Summary
Bio::ClusterIO::unigene - UniGene input stream
Package variables
Privates (from "my" definitions)
%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{^//},)
Included modules
Bio::Cluster::ClusterFactory
Bio::Cluster::UniGene
Inherit
Bio::ClusterIO
Synopsis
Do not use this module directly. Use it via the Bio::ClusterIO class.
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.
Methods
_initialize
No description
Code
next_clusterDescriptionCode
Methods description
next_clustercode    nextTop
 Title	 : next_cluster
Usage : $unigene = $stream->next_cluster()
Function: returns the next unigene in the stream
Returns : Bio::Cluster::UniGene object
Args : NONE
Methods code
_initializedescriptionprevnextTop
sub _initialize {
	my($self, @args) = @_;

	$self->SUPER::_initialize(@args);
	if(! $self->cluster_factory()) {
	$self->cluster_factory(Bio::Cluster::ClusterFactory->new(
						-type => 'Bio::Cluster::UniGene'));
	}
}
next_clusterdescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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 BugsTop
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 - Andrew MacgregorTop
Email: andrew at cbbc.murdoch.edu.au
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _