epaule

#!/usr/bin/env perl
use Ace;
use Getopt::Long;

my @genes;
my $database;

GetOptions('gene=s' => \@genes,
           'database=s' => \$database,
)||die(@!);

epaule

#!/usr/bin/env perl
# take a reference database and a handful of curation ones and udpdate the reference_db

use strict;
use Getopt::Long;
use Ace;
use Ace::Sequence;

my $targetDB;

epaule

#!/usr/bin/env ruby

require 'bio'

ff= Bio::FlatFile.auto(ARGF)

ff.each_entry{|e|

	gap=''
	e.seq.to_s.scan(/N{10,}/) do |c|

epaule

#!/usr/bin/env ruby
# filter_fasta.rb blackllist fastafile
# blacklist will have one ID per line

require 'bio'

bl = Hash.new
#slurp in the blacklist
IO.foreach(ARGV.shift){|l|
  bl[l.chomp]=1

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

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/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 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 python
# random_sample_chooser.py <GFF3>
import re
import sys
import random

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

mRNAids = {}

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;