Bio::Index::EMBL(3) User Contributed Perl Documentation Bio::Index::EMBL(3)NAMEBio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot
.dat files (i.e. flat file EMBL/Swissprot format).
SYNOPSIS
# Complete code for making an index for several
# EMBL files
use Bio::Index::EMBL;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::EMBL->new(-filename => $Index_File_Name,
-write_flag => 'WRITE');
$inx->make_index(@ARGV);
# Print out several sequences present in the index
# in Fasta format
use Bio::Index::EMBL;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::EMBL->new(-filename => $Index_File_Name);
my $out = Bio::SeqIO->new(-format => 'Fasta',-fh => \*STDOUT);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns 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
Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
and provides the basic funtionallity for indexing EMBL files, and
retrieving the sequence from them. Heavily snaffled from James Gilbert
and his Fasta system. Note: for best results 'use strict'.
The keys are the identifiers in the ID and AC lines.
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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
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:
http://bugzilla.open-bio.org/
AUTHOR - Ewan Birney
Email - birney@sanger.ac.uk
APPENDIX
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 EMBL format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
_file_format
Title : _file_format
Usage : Internal function for indexing system
Function: Provides file format for this database
Example :
Returns :
Args :
perl v5.14.1 2011-07-22 Bio::Index::EMBL(3)