NAME

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

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 funtionality 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/.

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;
   }

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:

  https://github.com/bioperl/bioperl-live/issues

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