epaule

#!/usr/bin/env ruby
require 'bio'

ff = Bio::FlatFile.new(Bio::GenBank, ARGF)
ff.each_entry{|gb|
  gb.each_cds{|cds|
    position = cds.position
    puts gb.naseq.splicing(position).to_fasta(cds.to_hash['protein_id'][0],60)
  }
}

epaule

#!/usr/bin/env perl

use Ace;

my $db = Ace->connect(-path => shift)||die(Ace::Error);

my $genes = $db->fetch_many(-query => 'find Gene Species="Pristionchus pacificus"; Ortholog');

while (my $gene = $genes->next){
  foreach my $o ($gene->Ortholog){

epaule

#!/usr/bin/perl
#
# dumps gene descriptions
#
# Options:
#   -format  <record || tab> (defaults to record)
#   -species <name>        WormBase species name
#   -store <storable file> pass a stored config
#   -debug <user>          send log mails to user
#   -test                  use the test database

epaule

#!/usr/bin/perl
#
# dumps all interactions into a flatfile, except the no_interaction ones
#

use Getopt::Long;
use Time::localtime;
use IO::File;
use Storable;

epaule

#!/software/bin/perl -w
#
# Small script to convert GF3 gene predictions to ace
#
# Last updated by: $Author: gw3 $     
# Last updated on: $Date: 2008/02/14 11:02:17 $      

use Getopt::Long;
use Carp;

epaule

#!/usr/bin/env python
# random_sample_chooser.py <GFF3>
import re
import sys
import random

gff=open(sys.argv[1],"r")

mRNAids = {}

epaule

#!/usr/bin/env perl
#
# exporter to dump gene / transcript / protein info as GPI file
#   specs: http://www.geneontology.org/page/gene-product-information-gpi-format
#
# uages:
#   perl dump_gpi.pl -species elegans


use strict;

epaule

#!/usr/bin/env perl
# dump the protein domains into a flatfile

use feature qw(say);

use Ace;
use strict;

my $db = Ace->connect(-path => shift)||die(Ace->error);

epaule

#!/usr/bin/env ruby
require 'net/https'
require 'uri'
 
require 'rubygems'
require 'json'
 
server = 'https://www.trackhubregistry.org'
hub_url = 'http://ftp.ebi.ac.uk/pub/databases/wormbase/releases/current-development-release/COMPARATIVE_ANALYSIS/hub/hub.txt'
user = 'michael.paulini'

epaule

#!/usr/bin/perl
# script.pl database file

use Ace;

my $db = Ace->connect(-path => shift);

while (<>){
   next unless /WBGene/;  # skip the header line
   s/\r\n//;                           # get rid of the mac line breaks