Summary

Bio::Index::Fasta - Interface for indexing (multiple) fasta files

Package variables

Included modules

Inherit

Bio::Index::AbstractSeq

Synopsis

    # Complete code for making an index for several
    # 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);

    # Print out several sequences present in the index
    # in Fasta format
    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
Details on configuration and additional example code are available in the
biodatabases.pod file, scripts/index/*PLS and in 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.

Methods

Methods description

 Title   : _file_format
 Function: The file format for this package, which is needed
           by the SeqIO system when reading the sequence.
 Returns : 'Fasta'

  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    :

  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

  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

sub _version {

    return 0.2;

}

sub _file_format {

    return 'Fasta';

}

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.
        );

    $begin = 0;

    my $id_parser = $self->id_parser;

    open FASTA, $file or $self->throw("Can't open file for read : $file");

    # Main indexing loop
    while (<FASTA>) {
        if (/^>/) {
            # $begin is the position of the first character after the '>'
            my $begin = tell(FASTA) - length( $_ ) + 1;
	    
            foreach my $id (&$id_parser($_)) {
		$self->add_record($id, $i, $begin);
            }
        }
    }

    close FASTA;
    return 1;

}

sub id_parser {

    my( $self, $code ) = @_;
    
    if ($code) {
        $self->{'_id_parser'} = $code;
    }
    return $self->{'_id_parser'} ||\& default_id_parser;

}

sub default_id_parser {

        if ($_[0] =~ /^>\s*(\S+)/) {
        return $1;
    } else {
        return;
    }

}

General documentation

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/MailList.shtml - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email - jgrg@sanger.ac.uk

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _