gisleDK

#!/bin/sh
# Script for merging fastq read counts
# Written by Gisle Vestergaard
# gisle@bio.ku.dk
[ $# != 2 ] && { echo "Usage: read_counter.sh <directory containing .fastq files DIR> <output filename FILE>"; exit 1; }
READDIR=$1
OUTPUT=$2
cd $READDIR
[ -e $OUTPUT ] && { echo "output file exists"; exit 1; }

gisleDK

#!/bin/ruby
# Script for adding hmmsearch results to Prodigal style gff files
# Written by Gisle Vestergaard
# gisle@bio.ku.dk

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

File.open(hmmsearch_file) do |ios|

gisleDK

#!/bin/ruby
# Script for organizing clusters from mcl
# Written by Gisle Vestergaard
# gisle@bio.ku.dk

ARGF.each_with_index do |line, count|
        plus = count+1
        fields = line.chomp.split("\t")
        puts plus.to_s + "\t" + line
end

gisleDK

#!/usr/bin/env ruby
# Qiime2: Merging several DADA2 denoised run feature tables and representative sequences for Qiime version 2017.12
# Feature tables must be name *_table.qza and representative sequences *_rep-seqs.qza
# V1.00 Written by Gisle Vestergaard

require 'pp'
require 'optparse'

tables = []
seqs   = []

gisleDK

#!/bin/zsh
# Script for merging multiple DADA2 denoised Illumina runs
# Provide file "runs.list" containing list of runs
# File names has to be <run>_table.qza and <run>_rep-seqs.qza
# Written by Gisle Vestergaard
# Email: gisle@bio.ku.dk

zmodload zsh/mapfile
runs=( ${(f)mapfile[$PWD/runs.list]} )

gisleDK

m54141_170208_104237/9699895/ccs
CTCAGGGTTGCAGCGAAATTTCAAGCGCCACTTCCGGGAATCTCAGAGCGATCTCGAAAGGAAGGGTACTTGTCTCTTAAGTCGCGGTAGGCCTTCATATAGCGACCTGCCTGCGCATCATCCACACAGGCGGACGCTCCAGAACTTTATTCTGTGCCGCTTGCAATAAACGAGGAACATTCTGAGCCGATCCAACTGTCATGTAGGTTATGTCTCCATCTCAAAAAGCAACCCCTATCGCATTCTACGATTTGTGGCGTCACTATCGCTGTAGATTGGCAAAGCTGGGTTGTTATTGCTAAGACTGTTGTTGTAGATACTTCACCCCAACCTCAGGTTGGTTATCTTTAAGCATTGAGTATAAATTAGTAGTATAAATCCTTAAGAAACTTTAAAAAAGGTTTAGAATTAGTGTGGTGAGTGGGAGACTAGTATGTTTCTAAGACTTGCAGACCAACATCGTCAATTTGTTCGAGATCTAGTAATGAGCCTTCGAGCTATGGCAATTGTCCTAGAGCGTCGAGGCTATATTGCTTCTTGCTACAACACCTGCGGCAGCCAAATGAACAGCGCTTCATTCATGGCAAGCCTAGGGGATAACCATCTAATCCGGTTTCTGGTGTCAGATTATGGGATTACCTGGACTGAAATGCGGGATGATCGAGAACTGATGAAGCTGGAAGGGGCCGAGGCAATTAGCCAGCTTCAAGAGTTAGCTGACTTAGTTAAATATCACAGTGAGAGCTTTGAAGAGCAGCCAGTTCTGATAAATTAAGCCTAACGAGTTTAATTCAGAGTCACTACTTTAGGAACAGTCACGAGCCGGACTCATGTCGTAATTATCGTGAGTGATAGGGTTATAGTTGGAGATGGCCCTTAGACCCAACTGTATTTCATGACTGCTTTGATTCTGGATGGCAACATCAACGTATCGAGACAAACCGATTCGACTGCATTGTGTTACGCAGGGAGACGGTGATTTAGTTCTGCT

gisleDK

#!/usr/bin/env ruby2.2
#
# This program take output from Diamond output run against EGGNOG databases and give COG information
# V1.00 Written by Gisle Vestergaard
require 'pp'
require 'optparse'

ARGV << '-h' if ARGV.empty?

options = {}

gisleDK

# @impl: Nonpareil
# @ksize: 32644
# @version: 3.00
# @maxL: 100
# @L: 88.496
# @R: 500
# @overlap: 50.00
# @divide: 0.70
0       0.00000 0.00000 0.00000 0.00000 0.00000
2       0.00000 0.00000 0.00000 0.00000 0.00000

gisleDK

#!/usr/bin/env ruby2.2

require 'pp'
require 'optparse'

ARGV << "-h" if ARGV.empty?

cmd_init = File.basename($0) + " " + ARGV.join(" ")

options = {}

gisleDK

#!/usr/bin/env ruby
# qsub parametres:
# Specify Ruby
#$ -S /usr/bin/ruby
# name for job
#$ -N blat
# pe request for slots, means processors, with
# minimum to maximum.
# e.g. 2    means two processors
#      2-   means 2 upto number of processor restricted by pe