maasha

#!/usr/bin/env ruby

require 'pp'

prodigal_file  = ARGV[0]
hmmsearch_file = ARGV[1]
hash_id        = {}

File.open(hmmsearch_file) do |ios|
  ios.each_line do |line|

maasha

#!/usr/bin/env perl

# Martin A. Hansen (mail@maasha.dk), September 2011

use strict;
use warnings;

use IPC::Open2;
use File::Which;

maasha

#!/usr/bin/env ruby

require 'pp'
require 'maasha/fastq'
require 'maasha/seq'

map_file = "/home/maasha/Data/KimMagnussen/20130904_hiseq2a_rescue/sample_table.txt"

barcode_hash  = {}
barcode1_hash = {}

maasha

#!/usr/bin/env ruby

require 'narray'

# http://en.wikipedia.org/wiki/Nucleic_acid_notation

nuc_str = "ACGTUWSMKRYBDHVNacgtuwsmkrybdhvn"
bin_str = "\x08\x04\x02\x01\x01\x09\x06\x0c\x03\x0a\x05\x07\x0b\x0d\x0e\x0f\x08\x04\x02\x01\x01\x09\x06\x0c\x03\x0a\x05\x07\x0b\x0d\x0e\x0f"

str1 = "ATCGatcg"

maasha

#!/usr/bin/perl -w

use strict;
use Getopt::Long;
use Data::Dumper;

# Lea Benedicte Skov Hansen, Apr May 2013

# Variables that should eventually be defined by user!!

maasha

#!/usr/bin/perl -w

use strict;
use Getopt::Long;
use Data::Dumper;

# Lea Benedicte Skov Hansen, Apr May 2013

# Variables that should eventually be defined by user!!

maasha

#!/usr/bin/perl -w

use strict;
use Getopt::Long;
use Data::Dumper;

# Lea Benedicte Skov Hansen, Apr May 2013

# Variables that should eventually be defined by user!!

maasha

Failures:

  1) Scaffold pages show 
     Failure/Error: visit scaffold_path(user, scaffold)
     ActiveRecord::RecordNotFound:
       Couldn't find Scaffold with id=2 [WHERE "scaffolds"."user_id" = 2]
     # ./app/controllers/scaffolds_controller.rb:9:in `show'
     # ./spec/requests/scaffold_pages_spec.rb:45:in `block (3 levels) in <top (required)>'

  2) Scaffold pages show 

maasha

class User < ActiveRecord::Base 
  attr_accessible :email, :name, :password, :password_confirmation
  has_secure_password
  has_many :scaffolds, dependent: :destroy
  
  before_save { |user| user.email = email.downcase }
  before_save :create_remember_token
  
  VALID_EMAIL_REGEX = /\A[\w+\-.]+@[a-z\d\-.]+\.[a-z]+\z/i
  PER_PAGE          = 30   # for pagination

maasha

rake routes
        users GET    /users(.:format)              users#index
              POST   /users(.:format)              users#create
     new_user GET    /users/new(.:format)          users#new
    edit_user GET    /users/:id/edit(.:format)     users#edit
         user GET    /users/:id(.:format)          users#show
              PUT    /users/:id(.:format)          users#update
              DELETE /users/:id(.:format)          users#destroy