lib/Bio/DB/SeqI.pm

   1 #
   2 # BioPerl module for Bio::DB::SeqI.pm
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Ewan Birney <birney@ebi.ac.uk>
   7 #
   8 # Copyright Ewan Birney
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11 #
  12
  13
  14 =head1 NAME
  15
  16 Bio::DB::SeqI - Abstract Interface for Sequence databases
  17
  18 =head1 SYNOPSIS
  19
  20    # get a Bio::DB::SeqI somehow
  21
  22    $seq = $seqdb->get_Seq_by_id('some-id');
  23    $seq = $seqdb->get_Seq_by_acc('some-accession-number');
  24
  25    @ids = $seqdb->get_all_ids();
  26    $stream = $seqdb->get_PrimarySeq_stream();
  27    while((my $seq = $stream->next_seq()) {
  28       # $seq is a PrimarySeqI compliant object
  29    }
  30
  31 =head1 DESCRIPTION
  32
  33 Abstract interface for a sequence database
  34
  35 =head1 FEEDBACK
  36
  37 =head2 Mailing Lists
  38
  39 User feedback is an integral part of the evolution of this and other
  40 Bioperl modules. Send your comments and suggestions preferably to one
  41 of the Bioperl mailing lists. Your participation is much appreciated.
  42
  43   bioperl-l@bioperl.org                  - General discussion
  44   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  45
  46 =head2 Support
  47
  48 Please direct usage questions or support issues to the mailing list:
  49
  50 I<bioperl-l@bioperl.org>
  51
  52 rather than to the module maintainer directly. Many experienced and
  53 reponsive experts will be able look at the problem and quickly
  54 address it. Please include a thorough description of the problem
  55 with code and data examples if at all possible.
  56
  57 =head2 Reporting Bugs
  58
  59 Report bugs to the Bioperl bug tracking system to help us keep track
  60 the bugs and their resolution.  Bug reports can be submitted via the
  61 web:
  62
  63   https://github.com/bioperl/bioperl-live/issues
  64
  65 =head1 AUTHOR - Ewan Birney
  66
  67 Email birney@ebi.ac.uk
  68
  69 =head1 APPENDIX
  70
  71 The rest of the documentation details each of the object methods. Internal
  72 methods are usually preceded with a _
  73
  74 =cut
  75
  76
  77 package Bio::DB::SeqI;
  78
  79 use strict;
  80
  81 use base qw(Bio::DB::RandomAccessI);
  82
  83 =head1 Methods inherited from Bio::DB::RandomAccessI
  84
  85 =head2 get_Seq_by_id
  86
  87  Title   : get_Seq_by_id
  88  Usage   : $seq = $db->get_Seq_by_id('ROA1_HUMAN')
  89  Function: Gets a Bio::Seq object by its name
  90  Returns : a Bio::Seq object
  91  Args    : the id (as a string) of a sequence
  92  Throws  : "id does not exist" exception
  93
  94 =head2 get_Seq_by_acc
  95
  96  Title   : get_Seq_by_acc
  97  Usage   : $seq = $db->get_Seq_by_acc('X77802');
  98  Function: Gets a Bio::Seq object by accession number
  99  Returns : A Bio::Seq object
 100  Args    : accession number (as a string)
 101  Throws  : "acc does not exist" exception
 102
 103 =head2 get_Seq_by_version
 104
 105  Title   : get_Seq_by_version
 106  Usage   : $seq = $db->get_Seq_by_version('X77802.1');
 107  Function: Gets a Bio::Seq object by sequence version
 108  Returns : A Bio::Seq object
 109  Args    : accession.version (as a string)
 110  Throws  : "acc.version does not exist" exception
 111
 112 =head1 Methods [that were] specific for Bio::DB::SeqI
 113
 114 =head2 get_PrimarySeq_stream
 115
 116  Title   : get_PrimarySeq_stream
 117  Usage   : $stream = get_PrimarySeq_stream
 118  Function: Makes a Bio::SeqIO compliant object
 119            which provides a single method, next_seq
 120  Returns : Bio::SeqIO
 121  Args    : none
 122
 123 =cut
 124
 125 sub get_PrimarySeq_stream{
 126    my ($self,@args) = @_;
 127    $self->throw("Object did not provide a PrimarySeq stream object");
 128 }
 129
 130
 131 =head2 get_all_primary_ids
 132
 133  Title   : get_all_ids
 134  Usage   : @ids = $seqdb->get_all_primary_ids()
 135  Function: gives an array of all the primary_ids of the
 136            sequence objects in the database. These
 137            may be ids (display style) or accession numbers
 138            or something else completely different - they
 139            *are not* meaningful outside of this database
 140            implementation.
 141  Example :
 142  Returns : an array of strings
 143  Args    : none
 144
 145 =cut
 146
 147 sub get_all_primary_ids{
 148    my ($self,@args) = @_;
 149    $self->throw("Object did not provide a get_all_ids method");
 150 }
 151
 152
 153 =head2 get_Seq_by_primary_id
 154
 155  Title   : get_Seq_by_primary_id
 156  Usage   : $seq = $db->get_Seq_by_primary_id($primary_id_string);
 157  Function: Gets a Bio::Seq object by the primary id. The primary
 158            id in these cases has to come from $db->get_all_primary_ids.
 159            There is no other way to get (or guess) the primary_ids
 160            in a database.
 161
 162            The other possibility is to get Bio::PrimarySeqI objects
 163            via the get_PrimarySeq_stream and the primary_id field
 164            on these objects are specified as the ids to use here.
 165  Returns : A Bio::Seq object
 166  Args    : accession number (as a string)
 167  Throws  : "acc does not exist" exception
 168
 169 =cut
 170
 171 sub get_Seq_by_primary_id {
 172    my ($self,@args) = @_;
 173    $self->throw("Abstract database call of get_Seq_by_primary_id. Your database".
 174        " has not implemented this method!");
 175
 176 }
 177
 178 1;
 179
 180
 181