Bio::Index::Swissprot

Description

Bio::Index::Swissprot is a Perl Interface for indexing (multiple) Swissprot .dat files (ie flat file swissprot format). SYNOPSIS # Complete code for making an index for several # Swissprot files use Bio::Index::Swissprot; use strict; my $Index_File_Name = shift; my $inx = Bio::Index::Swissprot->new(-filename => $Index_File_Name, -write_flag => WRITE); $inx->make_index(@ARGV); # Print out several sequences present in the index # in gcg format use Bio::Index::Swissprot; use Bio::SeqIO; use strict; my $out = Bio::SeqIO->new( -format => gcg, -fh => *STDOUT ); my $Index_File_Name = shift; my $inx = Bio::Index::Swissprot->new(-filename => $Index_File_Name); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns Bio::Seq object $out->write_seq($seq); } # alternatively my ($id, $acc); my $seq1 = $inx->get_Seq_by_id($id); my $seq2 = $inx->get_Seq_by_acc($acc); Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing Swissprot files, and retrieving the sequence from them. Heavily snaffled from James Gilberts Fasta system. Note: for best results use strict. Details on configuration and additional example code are available in the biodatabases.pod file..

Perl Interface - Swissprot Dat - Bioindexswissprot - Flat File - Swissprot - File - Index - Files - Id - Indexing - Libraries - Programming

Published By:Ewan Birney

License Type:Freeware

Date Added:22 October, 2010

Version:1.4

Price:Free

Downloads:74

Size:4.7 MB

Platform: Linux

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