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So I am trying to run a program iRep and usually it runs as-

iRep -f Bins/10000A-01-01_bin.* -s sam/10000A-01-01.sam.sorted.sam --sort -o 10000A-01-01_iRep_output

in sam folder -

10000A-01-01.sam.sorted.sam
10000A-01-02.sam.sorted.sam
10000A-01-03.sam.sorted.sam

in Bins folder -

10000A-01-01_bin.1.fa
10000A-01-01_bin.2.fa
10000A-01-01_bin.3.fa

10000A-01-02_bin.1.fa
10000A-01-02_bin.2.fa
10000A-01-02_bin.3.fa

10000A-01-03_bin.1.fa
10000A-01-03_bin.3.fa
10000A-01-03_bin.5.fa
10000A-01-03_bin.7.fa

I want to have one loop where I can do all in one command, instead of running each command for each sample individually, like

iRep -f Bins/10000A-01-01_bin.* -s sam/10000A-01-01.sam.sorted.sam --sort -o 10000A-01-01_iRep_output
iRep -f Bins/10000A-01-02_bin.* -s sam/10000A-01-02.sam.sorted.sam --sort -o 10000A-01-02_iRep_output
iRep -f Bins/10000A-01-03_bin.* -s sam/10000A-01-03.sam.sorted.sam --sort -o 10000A-01-03_iRep_output

Any idea how I could do this?

2 Answers 2

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#!/bin/sh

# Loop over the SAM files
for sam in sam/*.sam.sorted.sam; do
    # Extract the sample name by taking the basename of the SAM file
    # and removing the known filename suffix.
    sample=$(basename "$sam" .sam.sorted.sam)

    # Call iRep (as described in the question)
    iRep -f Bins/"$sample"_bin.* -s "$sam" --sort -o "$sample"_iRep_output
done

Given the files in the question, this would end up running

iRep -f Bins/10000A-01-01_bin.1.fa Bins/10000A-01-01_bin.2.fa Bins/10000A-01-01_bin.3.fa -s sam/10000A-01-01.sam.sorted.sam --sort -o 10000A-01-01_iRep_output
iRep -f Bins/10000A-01-02_bin.1.fa Bins/10000A-01-02_bin.2.fa Bins/10000A-01-02_bin.3.fa -s sam/10000A-01-02.sam.sorted.sam --sort -o 10000A-01-02_iRep_output
iRep -f Bins/10000A-01-03_bin.1.fa Bins/10000A-01-03_bin.3.fa Bins/10000A-01-03_bin.5.fa -s sam/10000A-01-03.sam.sorted.sam --sort -o 10000A-01-03_iRep_output
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  • can we make the above scripts in parallel? @Kusalananda
    – shanky
    Sep 24, 2019 at 9:42
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Using GNU Parallel it looks like this:

parallel --plus iRep -f Bins/{/...}_bin.* -s {} --sort -o {/...}_iRep_output ::: sam/*.sam.sorted.sam

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