diff variant_effect_predictor/Bio/Biblio/IO/pubmed2ref.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Biblio/IO/pubmed2ref.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,144 @@
+# $Id: pubmed2ref.pm,v 1.2 2002/10/22 07:45:13 lapp Exp $
+#
+# BioPerl module Bio::Biblio::IO::pubmed2ref.pm
+#
+# Cared for by Martin Senger <[e-mail]>
+# For copyright and disclaimer see below.
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Biblio::IO::pubmed2ref - A converter of a raw hash to PUBMED citations
+
+=head1 SYNOPSIS
+
+ # to be written
+
+=head1 DESCRIPTION
+
+ # to be written
+
+=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
+the Bioperl mailing list.  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
+of the bugs and their resolution. Bug reports can be submitted via
+email or the web:
+
+  [e-mail]
+  http://bugzilla.bioperl.org/
+
+=head1 AUTHOR
+
+Martin Senger ([e-mail])
+
+=head1 COPYRIGHT
+
+Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.
+
+This module is free software; you can redistribute it and/or modify
+it under the same terms as Perl itself.
+
+=head1 DISCLAIMER
+
+This software is provided "as is" without warranty of any kind.
+
+=head1 APPENDIX
+
+Here is the rest of the object methods.  Internal methods are preceded
+with an underscore _.
+
+=cut
+
+
+# Let the code begin...
+
+
+package Bio::Biblio::IO::pubmed2ref;
+
+use strict;
+use vars qw(@ISA $VERSION $Revision);
+
+use Bio::Biblio::IO::medline2ref;
+@ISA = qw(Bio::Biblio::IO::medline2ref);
+
+BEGIN { 
+    # set the version for version checking
+    $VERSION = do { my @r = (q$Revision: 1.2 $ =~ /\d+/g); sprintf "%d.%-02d", @r };
+    $Revision = q$Id: pubmed2ref.pm,v 1.2 2002/10/22 07:45:13 lapp Exp $;
+}
+
+# ---------------------------------------------------------------------
+#
+#   Here is the core...
+#
+# ---------------------------------------------------------------------
+
+sub _load_instance {
+    my ($self, $source) = @_;
+
+    my $result;
+    my $article = $$source{'article'};
+    if (defined $article) {
+	if (defined $$article{'journal'}) {
+	    $result = $self->_new_instance ('Bio::Biblio::PubmedJournalArticle');
+	    $result->type ('JournalArticle');
+	} elsif (defined $$article{'book'}) {
+	    $result = $self->_new_instance ('Bio::Biblio::PubmedBookArticle');
+	    $result->type ('BookArticle');
+	} else {
+	    $result->type ('PubmedArticle');
+	}
+    }
+    $result = $self->_new_instance ('Bio::Biblio::Ref') unless defined $result;
+    return $result;
+}
+
+sub convert {
+    my ($self, $source) = @_;
+    my $result = $self->SUPER::convert ($source->{'Citation'});	
+
+    # here we do PUBMED's specific stuff
+    my $pubmed_data = $$source{'PubmedData'};
+    if (defined $pubmed_data) {
+
+	# ... just take it (perhaps rename it)
+	$result->pubmed_status ($$pubmed_data{'publicationStatus'}) if defined $$pubmed_data{'publicationStatus'};
+	$result->pubmed_provider_id ($$pubmed_data{'providerId'}) if defined $$pubmed_data{'providerId'};
+	$result->pubmed_article_id_list ($$pubmed_data{'pubmedArticleIds'}) if defined $$pubmed_data{'pubmedArticleIds'};
+	$result->pubmed_url_list ($$pubmed_data{'pubmedURLs'}) if defined $$pubmed_data{'pubmedURLs'};
+
+	# ... put all dates from all 'histories' into one array
+	if (defined $$pubmed_data{'histories'}) {
+	    my @history_list;
+	    foreach my $history ( @{ $$pubmed_data{'histories'} } ) {
+		my $ra_pub_dates = $$history{'pubDates'};
+		foreach my $pub_date ( @{ $ra_pub_dates } ) {
+		    my %history = ();
+		    my $converted_date = &Bio::Biblio::IO::medline2ref::_convert_date ($pub_date);
+		    $history{'date'} = $converted_date if defined $converted_date;
+		    $history{'pub_status'} = $$pub_date{'pubStatus'} if defined $$pub_date{'pubStatus'};
+		    push (@history_list, \%history);
+		}
+	    }
+	    $result->pubmed_history_list (\@history_list);
+	}
+    }
+
+    # Done!
+    return $result;
+}
+
+1;
+__END__