Bio::Index Fasta
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Summary
Bio::Index::Fasta - Interface for indexing (multiple) fasta files
Package variables
No package variables defined.
Included modules
Bio::Seq
Inherit
Bio::Index::AbstractSeq
Synopsis
    # Make an index for one or more fasta files
use Bio::Index::Fasta;
use strict;
my $Index_File_Name = shift; my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name, -write_flag => 1); $inx->make_index(@ARGV); # Once the index is made it can accessed, either in the # same script or a different one use Bio::Index::Fasta; use strict; my $Index_File_Name = shift; my $inx = Bio::Index::Fasta->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); } # or, alternatively my $id; my $seq = $inx->get_Seq_by_id($id); # identical to fetch()
Description
Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
and provides the basic funtionallity for indexing fasta files, and
retrieving the sequence from them. For best results 'use strict'.
Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning
it can be used as a Sequence database for other parts of bioperl
Additional example code is available in scripts/index/*PLS and in
the Bioperl Tutorial (http://www.bioperl.org/wiki/Bptutorial.pl)
Note that by default the key for the sequence will be the first continuous
string after the '>' in the fasta header. If you want to use a specific
substring of the fasta header you must use the id_parser() method.
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
$inx->make_index($file_name);
# here is where the retrieval key is specified sub get_id { my $line = shift; $line =~ /^>.+gi\|(\d+)/; $1; }
Methods
_version
No description
Code
_file_formatDescriptionCode
_index_fileDescriptionCode
id_parserDescriptionCode
default_id_parserDescriptionCode
Methods description
_file_formatcode    nextTop
 Title   : _file_format
Function: The file format for this package, which is needed
by the SeqIO system when reading the sequence.
Returns : 'Fasta'
_index_filecodeprevnextTop
  Title   : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index FASTA format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
id_parsercodeprevnextTop
  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. Useful
for (for instance) specifying a different
parser for different flavours of FASTA file.
Returns \&default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fasta
description line. 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_parsercodeprevnextTop
  Title   : default_id_parser
Usage : $id = default_id_parser( $header )
Function: The default Fasta ID parser for Fasta.pm
Returns $1 from applying the regexp /^>\s*(\S+)/
to $header.
Returns : ID string
Args : a fasta header line string
Methods code
_versiondescriptionprevnextTop
sub _version {
    return 0.2;
}
_file_formatdescriptionprevnextTop
sub _file_format {
    return 'Fasta';
}
_index_filedescriptionprevnextTop
sub _index_file {
    my( $self,
         $file, # File name
$i, # Index-number of file being indexed
) = @_; my( $begin, # Offset from start of file of the start
# of the last found record.
); my $id_parser = $self->id_parser; open my $FASTA, '<', $file or $self->throw("Can't open file for read : $file"); my $offset = ( $^O =~ /mswin/i ) ? 1 : 0; # Main indexing loop
while (<$FASTA>) { if (/^>/) { # the following was fixed to allow validation - cjfields
# $begin is the position of the first character after the '>'
$begin = tell($FASTA) - length( $_ ) - $offset; foreach my $id (&$id_parser($_)) { $self->add_record($id, $i, $begin); } } } close $FASTA; return 1;
}
id_parserdescriptionprevnextTop
sub id_parser {
    my( $self, $code ) = @_;

    if ($code) {
        $self->{'_id_parser'} = $code;
    }
    return $self->{'_id_parser'} ||\& default_id_parser;
}
default_id_parserdescriptionprevnextTop
sub default_id_parser {
    if ($_[0] =~ /^>\s*(\S+)/) {
        return $1;
    } else {
        return;
    }
}

1;
}
General documentation
FEED_BACKTop
Mailing ListsTop
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 Top
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 BugsTop
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - James GilbertTop
Email - jgrg@sanger.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _