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cd $SCRATCH/core_ngs/fastq_prep
zcat Sample_Yeast_L005_R1.cat.fastq.gz | echo "$((`wc -l` / 4))"
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Note that arithmetic in the bash shell is integer valued only, so don't use it for anything that requires decimal places! |
A better way to do math
Well, doing math in bash is pretty awful – there has to be something better. There is! It's called awk, which is a powerful scripting language that is easily invoked from the command line.
In the code below we pipe the output from wc -l (number of lines in the FASTQ file) to awk, which executes its body (the statements between the curly braces ( { } ) for each line of input. Here the input is just one line, with one field – the line count. The awk body just divides the 1st input field ($1) by 4 and writes the result to standard output. (Read more about awk in Advanced commands: awk)
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cd $SCRATCH/core_ngs/fastq_prep
zcat Sample_Yeast_L005_R1.cat.fastq.gz | wc -l | awk '{print $1 / 4}'
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Processing multiple compressed files
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