telatin

#!/usr/bin/env bash
# Version 2.1.0
# QIB Cloud Documentation: https://quadram-institute.atlassian.net/servicedesk/customer/portal/3/article/4423859?src=1372879570
# this is for QIB cloud where user can sudo

# ======================================================================
# HINT: 
# Create a ~/.user file with storing your NBI username and password: 
# echo -e "username=XX\npassword=YY" > ~/.user
# ======================================================================

telatin

# https://forum.nim-lang.org/t/8162#52466

import strutils

proc floatSeparator(f: float, s=","): string =
  var s = ($f).split('.')
  s[0] = s[0].insertSep(',')
  return s.join(".") 

let

telatin

#Function to print to STDERR
echoerr() { echo "$@" 1>&2; }

telatin

export MODULEPATH='/your/path/to/modules'
case "$0" in
          -sh|sh|*/sh)  modules_shell=sh ;;
       -ksh|ksh|*/ksh)  modules_shell=ksh ;;
       -zsh|zsh|*/zsh)  modules_shell=zsh ;;
    -bash|bash|*/bash)  modules_shell=bash ;;
esac
module() { eval `/usr/bin/modulecmd $modules_shell $*`; }

telatin

#!/bin/bash
# Andrea Telatin 2017, Bash Training for Bioinformatics, Quadram Institute

# Defaults:
input_dir="./";
ext='fastq.gz'

# Usage:
echo " Merge Illumina lanes

telatin

#!/bin/bash
set -euo pipefail

FOR=CCTACGGGNGGCWGCAG
REV=GGACTACHVGGGTATCTAATCC

# Cutadapt options
MINL=250
EXTRA=" --report minimal  --cores 0 --discard-untrimmed  "

telatin

#!/usr/bin/env python3

# Parses a file with a list of URLs (GTR user) and prints
# a table with their projects details
import json
import sys
import traceback
import urllib3
import xmltodict
from pprint import pprint

telatin

library(dada2)
library(ggplot)
packageVersion("dada2")
library(ShortRead)
packageVersion("ShortRead")
library(Biostrings)
packageVersion("Biostrings")
path <- "/Volumes/Informatics/telatin/qibx/ITS/"
prmr_funcn <- function(prmr) {
  prmr_dna <- DNAString(prmr)

telatin

#!/usr/bin/env python3
"""
A program to check that a list of programs is avalable retrieving their versions, if required.
Example configuration JSON (by default will look for 'checker.json' in the same directory as the program itself):
{
  "binaries": {
    "Zip": {
      "params": ["-h"],
      "binary": "zip",
      "stdout": "Copyright",

telatin

Contig1	Contig2	Edge
Salmonella~virus~FSLSP030	k141_1850	82.900904361823
k141_1850	Salmonella~virus~FSLSP030	82.900904361823
Salmonella~virus~Chi	k141_1850	77.68907855001756
k141_1850	Salmonella~virus~Chi	77.68907855001756
Salmonella~virus~FSLSP088	k141_1850	74.64006567255709
k141_1850	Salmonella~virus~FSLSP088	74.64006567255709
Salmonella~phage~118970_sal1	k141_1850	74.42229632318072
k141_1850	Salmonella~phage~118970_sal1	74.42229632318072