maasha

#!/usr/bin/env ruby

require 'set'
require 'google_hash'
require 'benchmark'

set    = Set.new
hash   = Hash.new(0)
ghashd = GoogleHashDenseIntToInt.new
ghashs = GoogleHashSparseIntToInt.new

maasha

#!/usr/bin/env ruby

require 'biopieces'

p = BP.new.
read_fastq(input: "in1.fq", input2: "in2.fq").
clip_primer(primer: "GTGCCAGCMGCCGCGGTAA",  direction: :forward, mismatch_percent: 20, search_distance: 50).
clip_primer(primer: "GGACTACHVGGGTWTCTAAT", direction: :forward, mismatch_percent: 20, search_distance: 100).
trim_primer(primer: "GTGCCAGCMGCCGCGGTAA",  direction: :forward, mismatch_percent: 20, overlap_min: 1).
trim_primer(primer: "GGACTACHVGGGTWTCTAAT", direction: :forward, mismatch_percent: 20, overlap_min: 1).

maasha

# Function to assert no difference between
# two given files.
function assert_no_diff
{
    local src=$1
    local dst=$2

    if [ ! -f $src ]; then
        echo_red "FAIL"
        log "FAIL"

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!!