diff variant_effect_predictor/Bio/SeqFeature/Primer.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/SeqFeature/Primer.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,320 @@
+# $Id: Primer.pm,v 1.10 2002/10/30 14:21:58 heikki Exp $
+#
+# BioPerl module for Bio::SeqFeature::Primer
+#
+# Cared for by Chad Matsalla
+#
+# Copyright Chad Matsalla
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::SeqFeature::Primer - Primer Generic SeqFeature
+
+=head1 SYNOPSIS
+
+     A synopsis does not yet exist for this module.
+
+=head1 DESCRIPTION
+
+     A description does not yet exist for this module.
+
+=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 - Chad Matsalla
+
+Chad Matsalla E<lt>[e-mail]<gt>
+
+=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::SeqFeature::Primer;
+use vars qw(@ISA);
+use strict;
+
+use Bio::Root::Root;
+use Bio::SeqFeature::Generic;
+use Bio::Seq;
+use Dumpvalue qw(dumpValue);
+
+my $dumper = new Dumpvalue();
+
+
+@ISA = qw(Bio::Root::Root Bio::SeqFeature::Generic);
+
+
+
+=head2 new()
+
+ Title   : new()
+ Usage   :
+ Function:
+ Example :
+ Returns :
+ Args    : 
+Devel notes: I think that I want to accept a hash
+
+=cut
+
+
+sub new {
+     my ($class, @args) = @_;  
+     my %arguments = @args;
+     my $self = $class->SUPER::new(@args);
+          # these are from generic.pm, with which i started
+     $self->{'_parse_h'}       = {};
+     $self->{'_gsf_tag_hash'}  = {}; 
+          # things that belong with the primer
+     my ($sequence, $primer_sequence_id, $id) = 
+     $self->{'_gsf_seqname'} = $self->{primer_sequence_id};
+          # i am going to keep an array of the things that have been passed
+          # into the object on construction. this will aid retrieval of these
+          # things later
+     foreach my $argument (sort keys %arguments) {
+          if ($argument eq "-SEQUENCE" || $argument eq "-sequence") {
+               if (ref($arguments{$argument}) eq "Bio::Seq") {
+                    $self->{seq} = $arguments{$argument};
+               }
+               else {
+                    $self->{seq} = new Bio::Seq( -seq => $arguments{$argument},
+                                                  -id => $arguments{-id});
+               }
+               $self->{tags}->{$argument} = "A Bio::Seq. Use seq() to get this 'tag'";
+          }
+          else {
+               (my $fixed = $argument) =~ s/-//;
+               $self->{tags}->{$fixed} = $arguments{$argument};
+          }
+     }
+     if (!$self->{seq}) {
+          $self->throw("You must pass in a sequence to construct this object.");
+     }
+     
+               # a bunch of things now need to be set for this SeqFeature
+               # things like:
+                    # TARGET=513,26
+                    # PRIMER_FIRST_BASE_INDEX=1
+                    # PRIMER_LEFT=484,20
+          return $self;
+}
+
+
+=head2 seq()
+
+ Title   : seq()
+ Usage   : $seq = $primer->seq();
+ Function: Return the _entire_ sequence associated with this Primer. 
+ Returns : A Bio::Seq object
+ Args    : None.
+Develper Note: Do you want to be able to set the sequence associated with this
+     SeqFeature?
+
+=cut
+
+sub seq {
+     my $self = shift;
+     return $self->{seq};
+}
+
+
+
+=head2 all_tags()
+
+ Title   : all_tags()
+ Usage   : @tags = $primer->all_tags();
+ Function: Return a list of tag names for this Primer.
+ Returns : An array of strings representing the names of tags in this Primer
+ Args    : None.
+ Notes   : When the Bio::SeqFeature::Primer object is created, the user can
+     pass in an arbitrary hash containing key->value pairs. This is allowed
+     because I didn't want to assume that the user was trying to model a
+     primer3 construct. 
+
+=cut
+
+#'
+
+sub all_tags {
+     my $self = shift;
+     my @tags = sort keys %{$self->{tags}};
+     return @tags;
+}
+
+
+=head2 primary_tag()
+
+ Title   : primary_tag()
+ Usage   : $tag = $feature->primary_tag();
+ Function: Returns the string "Primer"
+ Returns : A string.
+ Args    : None.
+
+=cut
+
+sub primary_tag {
+     return "Primer";
+}
+
+=head2 source_tag()
+
+ Title   : source_tag()
+ Usage   : $tag = $feature->source_tag();
+ Function: Returns the source of this tag.
+ Returns : A string.
+ Args    : If an argument is provided, the source of this SeqFeature
+     is set to that argument.
+
+=cut
+
+sub source_tag {
+     my ($self,$insource) = @_;
+     if ($insource) { $self->{source} = $insource; }
+     return $self->{source};
+}
+
+=head2 has_tag()
+
+ Title   : has_tag()
+ Usage   : $true_or_false = $feature->has_tag('MELTING_TEMPERATURE');
+ Function: Does this SeqFeature have this tag?
+ Returns : TRUE or FALSE
+ Args    : A string.
+
+=cut
+
+sub has_tag {
+     my ($self,$tagname) = @_;
+     if ($self->{tags}->{$tagname}) { return "TRUE"; }
+     return { "FALSE" };
+}
+
+=head2 each_tag_value()
+
+ Title   : each_tag_value()
+ Usage   : $tag = $feature->each_tag_value('MELTING_TEMPERATURE');
+ Function: Returns the value of this tag.
+ Returns : Unknown. Whatever the value of the given tag was.
+ Args    : None.
+
+=cut
+
+sub each_tag_value {
+     my ($self,$tagname) = @_;
+     return $self->{tags}->{$tagname};
+}
+
+=head2 location()
+
+ Title   : location()
+ Usage   : $tag = $feature->location();
+ Function: returns a location object suitable for identifying location of
+     feature on sequence or parent feature  
+ Returns : a bio::locationi object.
+ Args    : none.
+Developer Notes: Chad has no idea how to implement this at this time.
+
+=cut
+
+sub location {
+     my $self = shift;
+     $self->warn("Chad has not written the code for this yet.");
+}
+
+=head2 start()
+
+ Title   : start()
+ Usage   : $start_position = $feature->start($new_position);
+ Function: Return the start position of this Primer.
+ Returns : The start position of this Primer.
+ Args    : If an argument is provided, the start position of this
+     Primer is set to that position.
+
+=cut
+
+sub start {
+     my ($self,$new_position) = @_;
+     if ($new_position) { $self->{start_position} = $new_position; }
+     return $self->{start_position};
+}
+
+=head2 end()
+
+ Title   : end()
+ Usage   : $end_position = $feature->end($new_position);
+ Function: Return the end position of this Primer.
+ Returns : The end position of this Primer.
+ Args    : If an argument is provided, the end position of this
+     Primer is set to that position.
+
+=cut
+
+sub end {
+     my ($self,$new_position) = @_;
+     if ($new_position) { $self->{end_position} = $new_position; }
+     return $self->{end_position};
+}
+
+=head2 strand()
+
+ Title   : strand()
+ Usage   : 
+ Function: 
+ Returns : 
+ Args    : 
+Developer Notes: Chad has no idea how to implement this at this time.
+
+=cut
+
+sub strand {
+     my $self = shift;
+     $self->warn("Chad has not implemented this method at this time.");
+}
+
+=head2 display_id()
+
+ Title   : display_id()
+ Usage   : $id = $feature->display_id($new_id)
+ Function: Returns the display ID for this Primer feature
+ Returns : A scalar.
+ Args    : If an argument is provided, the display_id of this Primer is
+     set to that value.
+
+=cut
+
+sub display_id {
+     my ($self,$newid) = @_;
+     if ($newid) { $self->seq()->display_id($newid); }
+     return $self->seq()->display_id();
+}
+
+
+1;