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set -e, -u, -o, -x pipefail

The set lines

• These lines deliberately cause your script to fail. Wait, what? Believe me, this is a good thing.
• With these settings, certain common errors will cause the script to immediately fail, explicitly and loudly. Otherwise, you can get hidden bugs that are discovered only when they blow up in production.

• set -euxo pipefail is short for:

set -e
set -u

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#!/usr/bin/env Rscript
#PBS -V

# This script will call copy number variants using cn.mops
# usage: Rscript cn.mops.R --help

library(optparse)
 
option_list = list(
  make_option(c("-i", "--input_dir"), type="character", default=NULL, 

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Bash best practices and style-guide

Just simple methods to keep the code clean.

Inspired by progrium/bashstyle and Kfir Lavi post.

Quick big rules

• All code goes in a function
• Always double quote variables

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stat_smooth_func <- function(mapping = NULL, data = NULL,
                        geom = "smooth", position = "identity",
                        ...,
                        method = "auto",
                        formula = y ~ x,
                       # show_formula = TRUE,     
                        se = TRUE,
                        n = 80,
                        span = 0.75,
                        fullrange = FALSE,

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# Run this script in a directory containing zip files from fastqc. It aggregates images of each type in individual folders
# So looking across data is quick.

zips=`ls *.zip`

for i in $zips; do
    unzip -o $i &>/dev/null;
done

fastq_folders=${zips/.zip/}

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Goal

• To create UniRef90 protein databases for NCBI blast and Diamond Blast
• To create a tab delimited taxid mapping file with two columns : sequenceID\tNCBITaxonID

Steps:

Download the uniref90 xml file first (warning - this is ~15 GB, will take a while)

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#!/bin/bash

# installs plenv, perl, carton, cpanminus, sets up environment in .bash_profile or .profile
# from https://github.com/tokuhirom/plenv#readme
MY_PROFILE_FILE="$HOME/.profile"

if [[ -n "$PERL_MB_OPT" ]]; then
    echo "You must unset your local::lib environment variables first"
    echo "Edit your ~/.bash_profile or ~/.bashrc and remove any references"
    echo "to local::lib or export PERL*..."

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#' call primer3 for a given set of DNAstringSet object
#' Forked from https://gist.github.com/al2na/8540391
#' TODO: Add support for target amplicon region (Maybe as [] in the fasta input)
#' @param seq: DNA template as a character string (required)
#' @param fw_primer: optional forward (left) primer, if provided Primer3 will assess it and will try to find a suitable reverse primer. Default: NULL
#' @param rv_primer: optional reverse (right) primer (must be reverse-complemented to the template), if provided Primer3 will assess it and will try to find a suitable forward primer. Default: NULL
#' @param size_range: a string with space separated list of desired amplicon size ranges. Default: '151-500'
#' @param Tm: range of melting temprature parameters as a numerical vector containing (min,optimal,max). default: c(55,57,58)
#' @param name: name of the amplicon in 'chr_start_end' format
#' @param sequence_target: a string containing space separated list of target pairs: 'starting_position,target_length starting_p