diff variant_effect_predictor/Bio/Seq/RichSeq.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/Seq/RichSeq.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,390 @@
+# $Id: RichSeq.pm,v 1.9 2002/11/11 18:16:31 lapp Exp $
+#
+# BioPerl module for Bio::Seq::RichSeq
+#
+# Cared for by Ewan Birney <[e-mail]>
+#
+# Copyright Ewan Birney
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Seq::RichSeq - Module implementing a sequence created from a rich
+sequence database entry
+
+=head1 SYNOPSIS
+
+See Bio::Seq::RichSeqI and documentation of methods.
+
+=head1 DESCRIPTION
+
+This module implements Bio::Seq::RichSeqI, an interface for sequences
+created from or created for entries from/of rich sequence databanks,
+like EMBL, GenBank, and SwissProt. Methods added to the Bio::SeqI
+interface therefore focus on databank-specific information. Note that
+not every rich databank format may use all of the properties provided.
+
+=head1 Implemented Interfaces
+
+This class implementes the following interfaces.
+
+=over 4
+
+=item Bio::Seq::RichSeqI
+
+Note that this includes implementing Bio::PrimarySeqI and Bio::SeqI.
+
+=item Bio::IdentifiableI
+
+=item Bio::DescribableI
+
+=item Bio::AnnotatableI
+
+=back
+
+=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://bio.perl.org/MailList.html             - 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 AUTHOR - Ewan Birney
+
+Email [e-mail]
+
+Describe contact details here
+
+=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::Seq::RichSeq;
+use vars qw($AUTOLOAD @ISA);
+use strict;
+
+# Object preamble - inherits from Bio::Root::Object
+
+use Bio::Seq;
+use Bio::Seq::RichSeqI;
+
+@ISA = qw(Bio::Seq Bio::Seq::RichSeqI);
+
+
+=head2 new
+
+ Title   : new
+ Usage   : $seq    = Bio::Seq::RichSeq->new( -seq => 'ATGGGGGTGGTGGTACCCT',
+                                             -id  => 'human_id',
+				             -accession_number => 'AL000012',
+				            );
+
+ Function: Returns a new seq object from
+           basic constructors, being a string for the sequence
+           and strings for id and accession_number
+ Returns : a new Bio::Seq::RichSeq object
+
+=cut
+
+sub new {
+    # standard new call..
+    my($caller,@args) = @_;
+    my $self = $caller->SUPER::new(@args);
+    
+    $self->{'_dates'} = [];
+    $self->{'_secondary_accession'} = [];
+
+    my ($dates, $xtra, $sv,
+	$keywords, $pid, $mol, 
+	$division ) = $self->_rearrange([qw(DATES 
+					   SECONDARY_ACCESSIONS
+					   SEQ_VERSION 
+					   KEYWORDS
+					   PID
+					   MOLECULE
+					   DIVISION
+					   )],
+				   @args);
+    defined $division && $self->division($division);
+    defined $mol && $self->molecule($mol);
+    defined $keywords && $self->keywords($keywords);
+    defined $sv && $self->seq_version($sv);
+    defined $pid && $self->pid($pid);
+
+    if( defined $dates ) {
+	if( ref($dates) =~ /array/i ) {
+	    foreach ( @$dates) {
+		$self->add_date($_);
+	    } 
+	} else { 
+	    $self->add_date($dates);
+	}
+    }
+
+    if( defined $xtra ) {
+	if( ref($xtra) =~ /array/i ) {
+	    foreach ( @$xtra) {
+		$self->add_secondary_accession($_);
+	    } 
+	} else { 
+	    $self->add_secondary_accession($xtra);
+	}
+    }
+    
+    return $self;
+}
+
+
+=head2 division
+
+ Title   : division
+ Usage   : $obj->division($newval)
+ Function: 
+ Returns : value of division
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub division {
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'_division'} = $value;
+    }
+    return $obj->{'_division'};
+
+}
+
+=head2 molecule
+
+ Title   : molecule
+ Usage   : $obj->molecule($newval)
+ Function: 
+ Returns : type of molecule (DNA, mRNA)
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub molecule {
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'_molecule'} = $value;
+    }
+    return $obj->{'_molecule'};
+
+}
+
+=head2 add_date
+
+ Title   : add_date
+ Usage   : $self->add_date($datestr)
+ Function: adds a date
+ Example :
+ Returns : a date string or an array of such strings
+ Args    :
+
+
+=cut
+
+sub add_date {
+   my ($self,@dates) = @_;
+   foreach my $dt ( @dates ) {
+       push(@{$self->{'_dates'}},$dt);
+   }
+}
+
+=head2 get_dates
+
+ Title   : get_dates
+ Usage   :
+ Function:
+ Example :
+ Returns : an array of date strings
+ Args    :
+
+
+=cut
+
+sub get_dates{
+   my ($self) = @_;
+   return @{$self->{'_dates'}}; 
+}
+
+
+=head2 pid
+
+ Title   : pid
+ Usage   :
+ Function: Get (and set, depending on the implementation) the PID property
+           for the sequence.
+ Example :
+ Returns : a string
+ Args    :
+
+
+=cut
+
+sub pid {
+    my ($self,$pid) = @_;
+    
+    if(defined($pid)) {
+	$self->{'_pid'} = $pid;
+    }
+    return $self->{'_pid'};
+}
+
+
+=head2 accession
+
+ Title   : accession
+ Usage   : $obj->accession($newval)
+ Function: Whilst the underlying sequence object does not 
+           have an accession, so we need one here.
+
+           In this implementation this is merely a synonym for
+           accession_number().
+ Example : 
+ Returns : value of accession
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub accession {
+   my ($obj,@args) = @_;
+   return $obj->accession_number(@args);
+}
+
+=head2 add_secondary_accession
+
+ Title   : add_secondary_accession
+ Usage   : $self->add_domment($ref)
+ Function: adds a secondary_accession
+ Example :
+ Returns : 
+ Args    : a string or an array of strings
+
+
+=cut
+
+sub add_secondary_accession {
+   my ($self) = shift;
+   foreach my $dt ( @_ ) {
+       push(@{$self->{'_secondary_accession'}},$dt);
+   }
+}
+
+=head2 get_secondary_accessions
+
+ Title   : get_secondary_accessions
+ Usage   :
+ Function:
+ Example :
+ Returns : An array of strings
+ Args    :
+
+
+=cut
+
+sub get_secondary_accessions{
+   my ($self,@args) = @_;
+   return @{$self->{'_secondary_accession'}}; 
+}
+
+=head2 seq_version
+
+ Title   : seq_version
+ Usage   : $obj->seq_version($newval)
+ Function: 
+ Example : 
+ Returns : value of seq_version
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub seq_version{
+   my ($obj,$value) = @_;
+   if( defined $value) {
+      $obj->{'_seq_version'} = $value;
+    }
+    return $obj->{'_seq_version'};
+
+}
+
+
+=head2 keywords
+
+ Title   : keywords
+ Usage   : $obj->keywords($newval)
+ Function: 
+ Returns : value of keywords (a string)
+ Args    : newvalue (optional) (a string)
+
+
+=cut
+
+sub keywords {
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'_keywords'} = $value;
+    }
+    return $obj->{'_keywords'};
+
+}
+
+#
+##
+### Deprecated methods kept for ease of transtion
+##
+#
+
+sub each_date {
+   my ($self) = @_;
+   $self->warn("Deprecated method... please use get_dates");
+   return $self->get_dates;
+}
+
+
+sub each_secondary_accession {
+   my ($self) = @_;
+   $self->warn("each_secondary_accession - deprecated method. use get_secondary_accessions");
+   return $self->get_secondary_accessions;
+
+}
+
+sub sv {
+   my ($obj,$value) = @_;
+   $obj->warn("sv - deprecated method. use seq_version");
+   $obj->seq_version($value);
+}
+
+
+1;