NAME
Bio::mGen - a fast and simple gene loading, helping automate BioPerl processes.
SYNOPSIS
use Bio::mGen;
print mGen::get_set();
or
print mGen::get_desc($as);
or
print mGen::get_list($as,$gn);
or
print mGen::get_gene($as);
or
print mGen::get_fasta($as);
or
print mGen::get_gene($as,$gn);
or
my $list=mGen::get_list($as,$gn);
my ($prot,$crc,$gene_index,$gn,$size,$range,$list,$pol,$desc,$xtra,)=split(/\|/,$list);
print "Gene: $gn, Size: $size, Polarity: $pol\nDescription: $desc\n\n";
or
mGen::reload_gene($as);
or
print "PRI division => ".$gb_division{PRI}."\n";
or
print "ACTG inverted is ".mGen::invert_dna('ACTG')."\n";
or
my ($start,$stop,%aa)=mGen::translate_table(11);
print "Start/Stop codons: $start \/ $stop, GGG equals $aa{GGG}\n";
print "ATGGATTACTGA => ".mGen::codon2aa("ATGGATTACTGA",$start,%aa)."\n";
DESCRIPTION
Bio::mGen
This module extracts pre-parsed compressed DNA from "Genbank" and "Refseq" (soon more) databases without draining the NCBI web server resources. Guaranteed to work faster than any module because of the features: Parse-free, compression ensuring twice twice faster download and reading from local disk, caching leading to instant load next time you use the data, and also mirroring.
Functions
get_desc
-
Gives AS's Desciption & summary.
get_list
-
List of genes' descriptions for the particular AS, gene name is optinal.
get_fasta
-
Reads particular AS whole sequence in fasta format.
get_gene
-
Reads parsed gene or list of genes for the particular AS. Gene name is optinal - leads to single gene output.
reload_gene
-
Updates the cache file.
translate_table
-
Loads the desirable translation table.
EXPORTS
Bio::mGen
exports the $db_path $base_path $imput_path $fasta_path $cache_path @mGen_urls $mGen_url %gb_division
by default, and $offset
by non-default.
AUTHOR
Ivan M Nanev, <cyber_indian at hotmail.com>
Bug reports welcome, patches even more welcome.