/ 
bioperl-1.2.2
/ Bio::Index::Fasta

NAME

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

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 $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. Note: for best results 'use strict'.

Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning it can be used a a Sequence database for other parts of bioperl

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/MailList.shtml - About the mailing lists

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 email or the web:

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

AUTHOR - James Gilbert

Email - jgrg@sanger.ac.uk

APPENDIX

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

_file_format

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

_index_file

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_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.  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_parser

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