unigene documentation.

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.*)/, EXPRESS => q///EXPRESS\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.*)/, DELIMITER => q///^\/\//)

sub next_cluster {

	my( $self) = @_;
	local $/ = "//";
	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{EXPRESS}/gcx) {
			my $express = $1;
			# remove initial semicolon if present
			$express =~ s/^;//; 
			@express = split /\s*;/, $express;
		}
		elsif ($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;
					$seq->{version} = $2 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;
				}								
			}
			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->express(\@express);
			$UGobj->gnm_terminus($unigene{GNM_TERMINUS}) if defined ($unigene{GNM_TERMINUS});
			$UGobj->chromosome(\@chromosome);
			$UGobj->sts(\@sts);
			$UGobj->txmap(\@txmap);
			$UGobj->protsim(\@protsim);
		}
	}
	return $UGobj;
}

1;

}

_initialize	No description	Code
next_cluster	Description	Code