Command Line Techniques

Secrets of the Der Lab

Volume 1: Guide to Kepler: shortcuts and hidden passageways

1. Aliases and environment variables for scripting

When developing a script it can be very help to slim down the time you spend typing in the same thing over and over and over and over and over and over and over and over again, which gets to be frustratingly boring! However, by using these secret shortcuts you'll really slim down the time you will have to spend doing all that boring stuff, PLUS it will make you feel like a computer wizard. It will seem like magic to onlookers, who just might say "Wait! what the heck did you just do there?". So give it a try! You might like it.

1. Aliases and environment variables

1a. make an environment variable for the path of the script

export S=/home/mcsimenc/scripts/apple-project/quant-snp-matrix.py

1b. making aliases that open scripts I'm currently working on

alias s='vim $S'

2. Always make a help for scripts that display when it is called with 0 arguments

This is how I do it in Python. Super simple, and can save you from frustration if you forget what you wrote a script for. Another line could be added for optional flags if you have any.

args = sys.argv
if len(args) < 2 or '-h' in args:
print('''
 usage:
	quant-snp-matrix.py <Psalmon> <STsalmon> <STmap> <Tsalmon> <Tmap>
	
 description:
 	merges expression and vcf data into single table
''', file=sys.stderr)
    sys.exit()

3. More Environment variables

When I was working on the script from #2, I did this to make trying it out easier,

export Psalmon=/home/mcsimenc/home2data/apple-pear/reference/MalusDomesticaAnnotation.PhytozomeV12/quantitation/salmon_output
export STsalmon=/home/mcsimenc/home2data/apple-pear/hiseq.huck.psu.edu/StringTieAssemblies/masked/salmon_quant/salmon_output
export STmap=/home/mcsimenc/home2data/apple-pear/hiseq.huck.psu.edu/StringTieAssemblies/masked/stringtie2phytozome.map

Then when you want to test the script you can simply do this,

$S $Psalmon $STsalmon $STmap

and if there was a bug, editing was as simple as

s

saves a lot of time.

4. Make environment variables of directories you currently work in and files you often use. For example, the paths to the reference genomes we're working on, which we need for many programs. MG1 for Malus domestica genome version 1

export A=/home/mcsimenc/home2data/apple-pear/hiseq.huck.psu.edu
export MG1=/home/mcsimenc/home2data/apple-pear/reference/reference_genome1/Mdomestica_196_v1.0.fa
export MG2=/home/mcsimenc/home2data/apple-pear/reference/reference_genome2/GDDH13_1-1_formatted.fasta

then you have shortcuts like this,

cd $A
cp $A/matt/test/newfile.txt .
ln -s $MG1

5. Make make environment settings for different projects as text files.

then you just have to load them if you're going to be working on that project,

source APPLE