Ivan M Nanev > mGen-1.03 > Bio::mGen

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mGen-1.03.tar.gz

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Module Version: 1.03   Source  

NAME ^

Bio::mGen - a fast and simple gene loading, helping automate BioPerl processes.

SYNOPSIS ^

  use Bio::mGen;

  print mGet_set();

or

  print mGet_desc($as);

or

  print mGet_list($as,$gn);

or

  print mGet_gene($as);

or

  print mGet_fasta($as);

or

  print mGet_gene($as,$gn);

or

  my $list=mGet_list($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.

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