Bio::Index::Fasta Bio::Index::Fasta is a Perl interface for indexing (multiple) fasta files.
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Perl module indexing Perl interface bio fasta fasta indexing

Bio::Index::Fasta Description

Bio::Index::Fasta is a Perl interface for indexing (multiple) fasta files. Bio::Index::Fasta is a Perl 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 $id; my $seq = $inx->get_Seq_by_id($id); #identical to fetchInherits 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 bioperlDetails 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. Requirements: · Perl

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