/ 
bioperl-0.05.1
/ 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;

my $Index_File_Name = shift;
my $inx = Bio::Index::Fasta->new($Index_File_Name, 'WRITE');
$inx->make_index(@ARGV);

# Print out several sequences present in the index
# in gcg format
use Bio::Index::Fasta;

my $Index_File_Name = shift;
my $inx = Bio::Index::Fasta->new($Index_File_Name);

foreach my $id (@ARGV) {
    my $seq = $inx->fetch($id); # Returns Bio::Seq object
    print $seq->layout('GCG');
}

# 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.

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.

vsns-bcd-perl@lists.uni-bielefeld.de          - General discussion
vsns-bcd-perl-guts@lists.uni-bielefeld.de     - Technically-oriented discussion
http://bio.perl.org/MailList.html             - 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://bio.perl.org/bioperl-bugs/

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 _

_initialize

Title   : _initialize
Usage   : $index->_initialize
Function: Calls $index->SUPER::_initialize(), and then adds
          the default id parser for fasta files.
Example : 
Returns : 
Args    :

_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    :

record_id

Title   : record_id
Usage   : $index->record_id( STRING );
Function: Parses the ID for an entry from the string
          supplied, using the code in $index->{'_id_parser'}
Example : 
Returns : scalar or exception
Args    : STRING

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.
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.
Example : 
Returns : ID string
Args    : a fasta header line string

fetch

Title   : fetch
Usage   : $index->fetch( $id )
Function: Returns a Bio::Seq object from the index
Example : $seq = $index->fetch( 'dJ67B12' )
Returns : Bio::Seq object
Args    : ID

get_Seq_by_id

Title   : get_Seq_by_id
Usage   : $seq = $db->get_Seq_by_id()
Function: retrieves a sequence object, identically to
          ->fetch, but here behaving as a Bio::DB::BioSeqI
Returns : new Bio::Seq object
Args    : string represents the id