SYNOPSIS
# Make an index for one or more Swissprot files:
use Bio::Index::Swissprot;
use strict;
my $index_file_name = shift;
my $inx = Bio::Index::Swissprot->new(
-filename => $index_file_name,
-write_flag => 1);
$inx->make_index(@ARGV);
# Print out several sequences present in the index in Genbank
# format:
use Bio::Index::Swissprot;
use Bio::SeqIO;
use strict;
my $out = Bio::SeqIO->new( -format => 'genbank',
-fh => \*STDOUT );
my $index_file_name = shift;
my $inx = Bio::Index::Swissprot->new(-filename => $index_file_name);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns a Bio::Seq object
$out->write_seq($seq);
}
# alternatively
my ($id, $acc);
my $seq1 = $inx->get_Seq_by_id($id);
my $seq2 = $inx->get_Seq_by_acc($acc);
DESCRIPTION
By default the index that is created uses the AC and ID identifiers as keys. This module inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic functionality for indexing Swissprot files and retrieving Sequence objects from them. For best results 'use strict'.You can also set or customize the unique key used to retrieve by writing your own function and calling the id_parser() method. For example:
$inx->id_parser(\&get_id); # make the index $inx->make_index($index_file_name); # here is where the retrieval key is specified sub get_id { my $line = shift; $line =~ /^KW\s+([A-Z]+)/i; $1; }
FEED_BACK
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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.
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 the web:
https://github.com/bioperl/bioperl-live/issues
AUTHOR - Ewan Birney
Also [email protected], bosborne at alum.mit.eduAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a __index_file
Title : _index_file Usage : $index->_index_file( $file_name, $i ) Function: Specialist function to index Swissprot format files. Is provided with a filename and an integer by make_index in its SUPER class. Example : Returns : Args :
id_parser
Title : id_parser Usage : $index->id_parser( CODE ) Function: Stores or returns the code used by record_id to parse the ID for record from a string. Returns \&default_id_parser (see below) if not set. An entry will be added to the index for each string in the list returned. Example : $index->id_parser( \&my_id_parser ) Returns : ref to CODE if called without arguments Args : CODE
default_id_parser
Title : default_id_parser Usage : $id = default_id_parser( $line ) Function: The default parser for Swissprot.pm Returns $1 from applying the regexp /^ID\s*(\S+)/ or /^AC\s+([A-Z0-9]+)/ to the current line. Returns : ID string Args : a line string
_file_format
Title : _file_format Usage : Internal function for indexing system Function: Provides file format for this database Example : Returns : Args :