bash: dynamical variables with multiple files in for loop

Question

I am working with some bash pipeline, which loop several pdb filles located in the receptors folder and post-process each file using some python script that required some expression defined as the flex_residues variable in the begining of the same scirpt:

home="$PWD"
receptors="${home}"/receptors
flex_residues='MET49_ASN142_CYS145_GLU166_GLN189'

# process each pdb file using the same %flex_residues 
for prot in "${receptors}"/*.pdb; do
receptor=$(basename "$prot" .pdb)
prepare_flexreceptor.py -r "${receptors}"/"${receptor}".pdb -s "${flex_residues}"
done

Now I would like to customize my pipeline to define different expressions of the $flex_residues depending on the processed pdb file. For example if I have 3 different pdb file in the receptors, I would like to define them in the begining of the script with the corresponded flex_residues. e.g.

receptor1.pdb >> flex_residues (for receptor1)='MET44_ASN142_CYS145_HIE163_GLN189'
receptor2.pdb >> flex_residues (for receptor 2) ='TRP12_ASN142_GLN188_GLU166_GLN189'
receptor3.pdb >> flex_residues (for receptor 3) ='ALA49_ASN142_MET111_HIS164_GLN189'

therefore the used flex_residues should automatically changes according to each processed receptor in the for loop. Could you suggest me the possibilities to modify my bash pipeline ?

tshiono · Accepted Answer · 2022-06-15 02:04:13Z

2

You can make use of an associative array. Would you please try:

#!/bin/bash

# initialize associative array
declare -A flex_residues=(
    ["receptor1"]="MET44_ASN142_CYS145_HIE163_GLN189"
    ["receptor2"]="TRP12_ASN142_GLN188_GLU166_GLN189"
    ["receptor3"]="ALA49_ASN142_MET111_HIS164_GLN189"
)

home="$PWD"
receptors="$home"/receptors

# process each pdb file using the same %flex_residues
for prot in "$receptors"/*.pdb; do
    receptor=$(basename "$prot" .pdb)
    if [[ -z ${flex_residues[$receptor]} ]]; then
        echo "No flex residue is defined for $receptor" >&2
    else
        prepare_flexreceptor.py -r "$temp/$receptor".pdbqt -s "${flex_residues[$receptor]}"
    fi
done

You can grow the declare line with as many lines as you want to initialize, or create a separate file which contains key-value pairs and read the file at the beginning of the script assigning the associative array.

edited Jun 15, 2022 at 2:04

answered Jun 14, 2022 at 9:10

tshiono

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4 Comments

James Starlight Over a year ago

thank you very much! very elegant solution. Does it mean that each pdb file (located in the receptors folder) should be defined in the associative array in the begining of the script?

Gordon Davisson Over a year ago

I'd recommend adding a test to make sure ${flex_residues[$receptor]} is defined before using it. Something like if [[ -z "${flex_residues[$receptor]}" ]]; then echo "No flex residue is defined for $receptor" >&2; continue; fi

tshiono Over a year ago

@GordonDavisson thank you for a nice suggestion. I've updated my answer accordingly.

tshiono Over a year ago

@JamesStarlight thank you for the feedback. As with scalar (non-array) variables, an array variable should be defined/assigned before it is referred. The assignment does not have to be at the very beginning of the script but it will be more readable to put the initialization in the beginning.

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