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What and why is Shell

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Scripting?

A shell is a program that takes your commands from the keyboard and gives them to the operating system. Most Linux systems utilize Bourne Again SHell (bash), but there are several additional shell programs on a typical Linux system such as ksh, tcsh, and zsh. The simplest way to check which shell your machine has is to type any random letters and hit enter. For example, Lonestar in TACC uses bash.

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The first real script you will likely find yourself wanting is one that performs a standard set of alignment tasks such as mapping, bam file creation and statistics reporting. The script below does exactly that using we want for the bwa aligner .would do the following:

1. Aligns a fastq file to a pre-made reference genome
2. Extracts alignments from bwa's proprietary binary .sai file to a .sam file
3. Converts the .sam file into a .bam file using samtools
4. Sort and index the .bam file so that it can be viewed in IGV.
5. Count the number of aligned and unaligned reads, and calculate the mapping rate.

The Example BWA alignment script takes

#!/bin/bash
echo "------------------------------------------";
echo "Define variables";
echo "------------------------------------------";
refPath="/Users/Daechan/Desktop/ref/sacCer1.fa";
inFile="subset.test.fastq"
PFX="subset.test.output"
saiFile="$PFX.sai";
samFile="$PFX.sam";
bamFile="$PFX.bam";

echo "Reference File: $refPath"
echo "Input File name: $inFile"
echo "Prefix for SAI BAM SAM files: $PFX"
echo "SAI file name: $saiFile"
echo "SAM file name: $samFile"
echo "BAM file name: $bamFile"

echo "------------------------------------------";
echo "Align subset.test.fastq on yeast genome";
echo "------------------------------------------";
bwa aln $refPath $inFile > $saiFile;
echo "...Done";
echo ""

echo "------------------------------------------";
echo "Convert the SAI file into the SAM file";
echo "------------------------------------------";
bwa samse $refPath $saiFile $inFile > $samFile;
echo "...Done";
echo ""

echo "------------------------------------------";
echo "Convert the SAM file into the BAM file";
echo "------------------------------------------";
samtools view -bS $samFile > $bamFile;
echo "...Done";
echo ""

echo "------------------------------------------";
echo "Calculate the simple statistics";
echo "------------------------------------------";
numMapRd=$(samtools view -F 0x04 $bamFile | wc -l );
echo "The number of mapped read: $numMapRd";
echo ""

numUnmapRd=$(samtools view -f 0x04 $bamFile | wc -l );
echo "The number of unmapped read: $numUnmapRd"
echo ""
echo "Mapping rate is : $[$[numMapRd*100]/$[numMapRd+numUnmapRd]]%"

Below is an example script for yeast. This works only in my machine because my yeast reference genome is under /Users/Daechan/Desktop/ref/ and the sample input file name is "subset.test.fastq" Change refPath and inFile variables, save as basic_script.sh, and execute it by entering "./basic_script.sh"

Exercise3

You can repeatedly use the above script for multiple datasets by allowing the script to take arguments. Below script will give you the same result as above. Plus, variant calling file (vcf) will be generated. Before execute the script, save the below lines as args_script.sh and enter "./args_script.sh" without arguments. It will give you information about positional arguments. If you want to map the input file "subset.test.fastq" onto yeast reference genome and put a prefix "test" on all output files, enter "./args_script.sh sacCer1 subset.test.fastq test

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Daechan original