diff variant_effect_predictor/Bio/SeqI.pm @ 0:1f6dce3d34e0

Uploaded

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+++ b/variant_effect_predictor/Bio/SeqI.pm	Thu Apr 11 02:01:53 2013 -0400
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+# $Id: SeqI.pm,v 1.25 2002/12/05 13:46:30 heikki Exp $
+#
+# BioPerl module for Bio::SeqI
+#
+# 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::SeqI [Developers] - Abstract Interface of Sequence (with features)
+
+=head1 SYNOPSIS
+
+    # Bio::SeqI is the interface class for sequences.
+
+    # If you are a newcomer to bioperl, you should
+    # start with Bio::Seq documentation. This
+    # documentation is mainly for developers using
+    # Bioperl.
+
+    # Bio::SeqI implements Bio::PrimarySeqI
+    $seq      = $seqobj->seq(); # actual sequence as a string
+    $seqstr   = $seqobj->subseq(10,50);
+
+    # Bio::SeqI has annotationcollections
+
+    $ann      = $seqobj->annotation(); # annotation object
+
+    # Bio::SeqI has sequence features
+    # features must implement Bio::SeqFeatureI
+
+    @features = $seqobj->get_SeqFeatures(); # just top level
+    @features = $seqobj->get_all_SeqFeatures(); # descend into sub features
+
+
+
+=head1 DESCRIPTION
+
+Bio::SeqI is the abstract interface of annotated Sequences. These
+methods are those which you can be guarenteed to get for any Bio::SeqI
+- for most users of the package the documentation (and methods) in
+this class are not at useful - this is a developers only class which
+defines what methods have to be implmented by other Perl objects to
+comply to the Bio::SeqI interface. Go "perldoc Bio::Seq" or "man
+Bio::Seq" for more information.
+
+
+There aren't many here, because too many complicated functions here
+prevent implementations which are just wrappers around a database or
+similar delayed mechanisms.
+
+Most of the clever stuff happens inside the SeqFeatureI system.
+
+A good reference implementation is Bio::Seq which is a pure perl
+implementation of this class with alot of extra pieces for extra
+manipulation.  However, if you want to be able to use any sequence
+object in your analysis, if you can do it just using these methods,
+then you know you will be future proof and compatible with other
+implementations of Seq.
+
+=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]
+
+
+=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::SeqI;
+use strict;
+
+use vars qw(@ISA);
+use Bio::PrimarySeqI;
+use Bio::AnnotatableI;
+use Bio::FeatureHolderI;
+
+# Object preamble - inheriets from Bio::PrimarySeqI
+
+@ISA = qw(Bio::PrimarySeqI Bio::AnnotatableI Bio::FeatureHolderI);
+
+=head2 get_SeqFeatures
+
+ Title   : get_SeqFeatures
+ Usage   : my @feats = $seq->get_SeqFeatures();
+ Function: retrieve just the toplevel sequence features attached to this seq
+ Returns : array of Bio::SeqFeatureI objects
+ Args    : none
+
+This method comes through extension of Bio::FeatureHolderI. See
+L<Bio::FeatureHolderI> and L<Bio::SeqFeatureI> for more information.
+
+=cut
+
+=head2 get_all_SeqFeatures
+
+ Title   : get_all_SeqFeatures
+ Usage   : @features = $annseq->get_all_SeqFeatures()
+ Function: returns all SeqFeatures, included sub SeqFeatures
+ Returns : an array of Bio::SeqFeatureI objects
+ Args    : none
+
+This method comes through extension of Bio::FeatureHolderI. See
+L<Bio::FeatureHolderI> and L<Bio::SeqFeatureI> for more information.
+
+=cut
+
+=head2 feature_count
+
+ Title   : feature_count
+ Usage   : $seq->feature_count()
+ Function: Return the number of SeqFeatures attached to a sequence
+ Returns : integer representing the number of SeqFeatures
+ Args    : none
+
+This method comes through extension of Bio::FeatureHolderI. See
+L<Bio::FeatureHolderI> for more information.
+
+=cut
+
+=head2 seq
+
+ Title   : seq
+ Usage   : my $string = $seq->seq();
+ Function: Retrieves the sequence string for the sequence object
+ Returns : string
+ Args    : none
+
+
+=cut
+
+sub seq{
+   my ($self) = @_;
+   $self->throw_not_implemented();
+}
+
+=head2 write_GFF
+
+ Title   : write_GFF
+ Usage   : $seq->write_GFF(\*FILEHANDLE);
+ Function: Convience method to write out all the sequence features
+           in GFF format to the provided filehandle (STDOUT by default)
+ Returns : none
+ Args    : [optional] filehandle to write to (default is STDOUT)
+
+
+=cut
+
+sub write_GFF{
+   my ($self,$fh) = @_;
+
+   $fh || do { $fh = \*STDOUT; };
+
+   foreach my $sf ( $self->get_all_SeqFeatures() ) {
+       print $fh $sf->gff_string, "\n";
+   }
+
+}
+
+=head2 annotation
+
+ Title   : annotation
+ Usage   : $obj->annotation($seq_obj)
+ Function: retrieve the attached annotation object
+ Returns : Bio::AnnotationCollectionI or none;
+
+See L<Bio::AnnotationCollectionI> and L<Bio::Annotation::Collection>
+for more information. This method comes through extension from
+L<Bio::AnnotatableI>.
+
+=cut
+
+=head2 species
+
+ Title   : species
+ Usage   :
+ Function: Gets or sets the species
+ Example : $species = $self->species();
+ Returns : Bio::Species object
+ Args    : Bio::Species object or none;
+
+See L<Bio::Species> for more information
+
+=cut
+
+sub species {
+    my ($self) = @_;
+    $self->throw_not_implemented();
+}
+
+=head2 primary_seq
+
+ Title   : primary_seq
+ Usage   : $obj->primary_seq($newval)
+ Function: Retrieve the underlying Bio::PrimarySeqI object if available.
+           This is in the event one has a sequence with lots of features
+           but want to be able to narrow the object to just one with
+           the basics of a sequence (no features or annotations).
+ Returns : Bio::PrimarySeqI
+ Args    : Bio::PrimarySeqI or none;
+
+See L<Bio::PrimarySeqI> for more information
+
+=cut
+
+sub primary_seq {
+    my ($self) = @_;
+    $self->throw_not_implemented;
+}
+
+1;