Skip to content

Instantly share code, notes, and snippets.

Avatar
💭
HackHackHack...

Martin Asser Hansen maasha

💭
HackHackHack...
View GitHub Profile
View prodigal_pfam_merger.rb
#!/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
maasha / sortfq
Last active Dec 24, 2015
Script for alphabetical sorting FASTQ files by their identifier. Example: `bzcat unsorted.fq.bz2 | sortfq | bzip2 > sorted.fq.bz2`
View sortfq
#!/usr/bin/env perl
# Martin A. Hansen (mail@maasha.dk), September 2011
use strict;
use warnings;
use IPC::Open2;
use File::Which;
@maasha
maasha / reconstruct_index.rb
Created Sep 19, 2013
Ruby script for the reconstruction of deteriorated index in paired end Illumina reads. maasha/seq and maasha/fastq are from www.biopieces.org
View reconstruct_index.rb
#!/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
maasha / hamming_dist.rb
Last active Dec 23, 2015
Hamming distance calculator taking into account IUPAC ambiguity codes for comparing two nucleotide sequenced the snappy way.
View hamming_dist.rb
#!/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"
View gist:5567819
#!/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!!
View gist:5567720
#!/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!!
View gist:5567347
#!/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!!
View gist:5386254
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
View gist:5362974
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
View gist:5362806
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