Bio/Index/Swissprot.pm

   1 #
   2 # BioPerl module for Bio::Index::Swissprot
   3 #
   4 # You may distribute this module under the same terms as perl itself
   5
   6 # POD documentation - main docs before the code
   7
   8 =head1 NAME
   9
  10 Bio::Index::Swissprot - Interface for indexing one or more
  11 Swissprot files.
  12
  13 =head1 SYNOPSIS
  14
  15   # Make an index for one or more Swissprot files:
  16
  17     use Bio::Index::Swissprot;
  18     use strict;
  19
  20     my $index_file_name = shift;
  21     my $inx = Bio::Index::Swissprot->new(
  22         -filename => $index_file_name,
  23         -write_flag => 1);
  24     $inx->make_index(@ARGV);
  25
  26   # Print out several sequences present in the index in Genbank
  27   # format:
  28
  29     use Bio::Index::Swissprot;
  30     use Bio::SeqIO;
  31     use strict;
  32
  33     my $out = Bio::SeqIO->new( -format => 'genbank',
  34                                -fh => \*STDOUT );
  35     my $index_file_name = shift;
  36     my $inx = Bio::Index::Swissprot->new(-filename => $index_file_name);
  37
  38     foreach my $id (@ARGV) {
  39         my $seq = $inx->fetch($id); # Returns a Bio::Seq object
  40         $out->write_seq($seq);
  41     }
  42
  43     # alternatively
  44     my ($id, $acc);
  45     my $seq1 = $inx->get_Seq_by_id($id);
  46     my $seq2 = $inx->get_Seq_by_acc($acc);
  47
  48 =head1 DESCRIPTION
  49
  50 By default the index that is created uses the AC and ID identifiers
  51 as keys. This module inherits functions for managing dbm files from
  52 Bio::Index::Abstract.pm, and provides the basic functionality
  53 for indexing Swissprot files and retrieving Sequence objects from
  54 them. For best results 'use strict'.
  55
  56 You can also set or customize the unique key used to retrieve by
  57 writing your own function and calling the id_parser() method.
  58 For example:
  59
  60    $inx->id_parser(\&get_id);
  61    # make the index
  62    $inx->make_index($index_file_name);
  63
  64    # here is where the retrieval key is specified
  65    sub get_id {
  66       my $line = shift;
  67       $line =~ /^KW\s+([A-Z]+)/i;
  68       $1;
  69    }
  70
  71 =head1 FEED_BACK
  72
  73 =head2 Mailing Lists
  74
  75 User feedback is an integral part of the evolution of this and other
  76 Bioperl modules. Send your comments and suggestions preferably to one
  77 of the Bioperl mailing lists.  Your participation is much appreciated.
  78
  79   bioperl-l@bioperl.org                  - General discussion
  80   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  81
  82 =head2 Support
  83
  84 Please direct usage questions or support issues to the mailing list:
  85
  86 I<bioperl-l@bioperl.org>
  87
  88 rather than to the module maintainer directly. Many experienced and
  89 reponsive experts will be able look at the problem and quickly
  90 address it. Please include a thorough description of the problem
  91 with code and data examples if at all possible.
  92
  93 =head2 Reporting Bugs
  94
  95 Report bugs to the Bioperl bug tracking system to help us keep track
  96 the bugs and their resolution.  Bug reports can be submitted via
  97 the web:
  98
  99   http://bugzilla.open-bio.org/
 100
 101 =head1 AUTHOR - Ewan Birney
 102
 103 Also lorenz@ist.org, bosborne at alum.mit.edu
 104
 105 =head1 APPENDIX
 106
 107 The rest of the documentation details each of the object methods.
 108 Internal methods are usually preceded with a _
 109
 110 =cut
 111
 112 # Let's begin the code...
 113
 114 package Bio::Index::Swissprot;
 115
 116 use strict;
 117
 118 use Bio::Seq;
 119
 120 use base qw(Bio::Index::AbstractSeq);
 121
 122 sub _type_stamp {
 123         return '__Swissprot_FLAT__'; # What kind of index are we?
 124 }
 125
 126 sub _version {
 127         return 0.1;
 128 }
 129
 130 =head2 _index_file
 131
 132   Title   : _index_file
 133   Usage   : $index->_index_file( $file_name, $i )
 134   Function: Specialist function to index Swissprot format files.
 135             Is provided with a filename and an integer
 136             by make_index in its SUPER class.
 137   Example :
 138   Returns :
 139   Args    :
 140
 141 =cut
 142
 143 sub _index_file {
 144         # $file is file name, $i is number of file being indexed
 145         my( $self, $file, $i ) = @_;
 146
 147         # Offset from start of file
 148         my $begin = 0;
 149
 150         my $id_parser = $self->id_parser;
 151
 152         open my $SWISSPROT,'<',$file or $self->throw("Can't read file: $file");
 153
 154         my %done_ids;
 155         while (<$SWISSPROT>) {
 156                 if (/^ID\s+\S+/) {
 157                         $begin = tell($SWISSPROT) - length( $_ );
 158                 }
 159                 for my $id (&$id_parser($_)) {
 160                         next if exists $done_ids{$id};
 161                         $self->add_record($id, $i, $begin) if $id;
 162                         $done_ids{$id} = 1;
 163                 }
 164         if (m{//}) {
 165             %done_ids = ();
 166         }
 167         }
 168         close $SWISSPROT;
 169         return 1;
 170 }
 171
 172 =head2 id_parser
 173
 174   Title   : id_parser
 175   Usage   : $index->id_parser( CODE )
 176   Function: Stores or returns the code used by record_id to
 177             parse the ID for record from a string.
 178             Returns \&default_id_parser (see below) if not
 179             set. An entry will be added to
 180             the index for each string in the list returned.
 181   Example : $index->id_parser( \&my_id_parser )
 182   Returns : ref to CODE if called without arguments
 183   Args    : CODE
 184
 185 =cut
 186
 187 sub id_parser {
 188         my( $self, $code ) = @_;
 189
 190         if ($code) {
 191                 $self->{'_id_parser'} = $code;
 192         }
 193         return $self->{'_id_parser'} || \&default_id_parser;
 194 }
 195
 196 =head2 default_id_parser
 197
 198   Title   : default_id_parser
 199   Usage   : $id = default_id_parser( $line )
 200   Function: The default parser for Swissprot.pm
 201             Returns $1 from applying the regexp /^ID\s*(\S+)/
 202             or /^AC\s+([A-Z0-9]+)/ to the current line.
 203   Returns : ID string
 204   Args    : a line string
 205
 206 =cut
 207
 208 sub default_id_parser {
 209         my $line = shift;
 210         if ($line =~ /^ID\s*(\S+)/) {
 211                 return $1;
 212         }
 213         elsif ($line =~ /^AC\s+([A-Z0-9]+)/) {
 214                 return $1;
 215         }
 216 }
 217
 218 =head2 _file_format
 219
 220  Title   : _file_format
 221  Usage   : Internal function for indexing system
 222  Function: Provides file format for this database
 223  Example :
 224  Returns :
 225  Args    :
 226
 227
 228 =cut
 229
 230 sub _file_format {
 231    return 'swiss';
 232 }
 233
 234 1;
 235
 236 __END__