diff variant_effect_predictor/Bio/DB/Ace.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/DB/Ace.pm	Thu Apr 11 02:01:53 2013 -0400
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+
+# $Id: Ace.pm,v 1.10 2002/10/22 07:38:29 lapp Exp $
+#
+# BioPerl module for Bio::DB::Ace
+#
+# 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::DB::Ace - Database object interface to ACeDB servers
+
+=head1 SYNOPSIS
+
+    $db = Bio::DB::Ace->new( -server => 'myace.server.com', port => '120000');
+
+    $seq = $db->get_Seq_by_id('MUSIGHBA1'); # Unique ID
+
+    # or ...
+
+    $seq = $db->get_Seq_by_acc('J00522'); # Accession Number
+
+=head1 DESCRIPTION
+
+This provides a standard BioPerl database access to Ace, using Lincoln Steins
+excellent AcePerl module. You need to download and install the aceperl module from
+
+  http://stein.cshl.org/AcePerl/
+
+before this interface will work.
+
+This interface is designed at the moment to work through a aceclient/aceserver
+type mechanism
+
+=head1 INSTALLING ACEPERL
+
+Download the latest aceperl tar file, gunzip/untar and cd into the directory.
+This is a standard CPAN-style directory, so if you go
+
+  Perl Makefile.PL
+  make
+  <become root>
+  make install
+
+Then you will have installed Aceperl. Use the PREFIX mechanism to install elsewhere.
+
+=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 AUTHOR - Ewan Birney
+
+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::DB::Ace;
+use vars qw(@ISA);
+use strict;
+
+# Object preamble - inherits from Bio::DB::RandomAccessI
+
+use Bio::DB::RandomAccessI;
+use Bio::Seq;
+
+BEGIN { 
+  eval {
+    require Ace;
+  };
+  if( $@) {
+    print STDERR "You have not installed Ace.pm.\n Read the docs in Bio::DB::Ace for more information about how to do this.\n It is very easy\n\nError message $@";
+  }
+}
+
+
+@ISA = qw(Bio::DB::RandomAccessI);
+
+# new() is inherited from Bio::DB::Abstract
+
+# _initialize is where the heavy stuff will happen when new is called
+
+sub new {
+  my($class,@args) = @_;
+  my $self = $class->SUPER::new(@args);
+  my ($host,$port) = $self->_rearrange([qw(
+					 HOST
+					 PORT
+					 )],
+				     @args,
+				     );
+
+  if( !$host || !$port ) {
+    $self->throw("Must have a host and port for an acedb server to work");
+  }
+
+  my $aceobj = Ace->connect(-host => $host,
+			    -port => $port) ||
+			      $self->throw("Could not make acedb object to $host:$port");
+
+  $self->_aceobj($aceobj);
+
+
+  return $self;
+}
+
+=head2 get_Seq_by_id
+
+ Title   : get_Seq_by_id
+ Usage   : $seq = $db->get_Seq_by_id($uid);
+ Function: Gets a Bio::Seq object by its unique identifier/name
+ Returns : a Bio::Seq object
+ Args    : $id : the id (as a string) of the desired sequence entry
+
+=cut
+
+sub get_Seq_by_id {
+  my $self = shift;
+  my $id = shift or $self->throw("Must supply an identifier!\n");
+  my $ace = $self->_aceobj();
+  my ($seq,$dna,$out);
+
+  $seq = $ace->fetch( 'Sequence' , $id);
+
+  # get out the sequence somehow!
+
+  $dna = $seq->asDNA();
+  
+  $dna =~ s/^>.*\n//;
+  $dna =~ s/\n//g;
+
+  $out = Bio::Seq->new( -id => $id, -type => 'Dna', -seq => $dna, -name => "Sequence from Bio::DB::Ace $id");
+  return $out;
+
+}
+
+=head2 get_Seq_by_acc
+
+  Title   : get_Seq_by_acc
+  Usage   : $seq = $db->get_Seq_by_acc($acc);
+  Function: Gets a Bio::Seq object by its accession number
+  Returns : a Bio::Seq object
+  Args    : $acc : the accession number of the desired sequence entry
+
+
+=cut
+
+sub get_Seq_by_acc {
+
+  my $self = shift;
+  my $acc = shift or $self->throw("Must supply an accesion number!\n");
+  
+  return $self->get_Seq_by_id($acc);
+}
+
+=head2 _aceobj
+
+  Title   : _aceobj
+  Usage   : $ace = $db->_aceobj();
+  Function: Get/Set on the acedb object 
+  Returns : Ace object
+  Args    : New value of the ace object
+
+=cut
+
+sub _aceobj {
+  my ($self,$arg) = @_;
+
+  if( $arg ) {
+    $self->{'_aceobj'} = $arg;
+  } 
+
+  return $self->{'_aceobj'};
+}
+
+1;
+
+
+
+
+
+