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

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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/ Email - jgrg@sanger.ac.uk 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