diff variant_effect_predictor/Bio/ClusterIO/unigene.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/ClusterIO/unigene.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,252 @@
+# $Id: unigene.pm,v 1.16.2.2 2003/09/15 01:50:47 andrew Exp $
+# BioPerl module for Bio::ClusterIO::unigene
+#
+# Cared for by Andrew Macgregor <[e-mail]>
+#
+# 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 doesn't 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.
+
+  [e-mail]			   - General discussion
+  http://bioperl.org/MailList.shtml - About the mailing lists
+
+=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 email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHORS - Andrew Macgregor
+
+Email: [e-mail]
+
+
+=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 vars qw(@ISA);
+use strict;
+
+use Bio::ClusterIO;
+use Bio::Cluster::UniGene;
+use Bio::Cluster::ClusterFactory;
+
+@ISA = 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.*)/,
+		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/^\/\//
+);
+
+# 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 $/ = "//";
+	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;
+