Counter in bash script

Question

I have a script that extracts filenames from an input file and is supposed to read each line (filename) and unzip the specified file, saving the unzipped content as individual files. However, I can't get my counter to work and just get all the unzipped files in one large file.

Input file contains a list: 
ens/484/59/traj.pdb 0.001353
ens/263/39/traj.pdb 0.004178
ens/400/35/traj.pdb 0.004191

I'm using the regex /.*?/.*?/ to extract the file that I'd like to unzip and name each output{1..40}.pdb -- instead I get one output file: output1.pdb which contains all the contents of the 40 unzipped files.

My question is: how do I correct my counter in order to achieve the desired naming scheme?

#!/bin/bash

file="/home/input.txt"
grep -Po '/.*?/.*?/' $file > filenames.txt
i=$((i+1))
structures='filenames.txt'

while IFS= read line
 do
   gunzip -c 'ens'$line'traj.pdb.gz' >> 'output'$i'.pdb'
 done <"$structures"

rm "$structures"

@EA00 Remember to double quote $line or else if it contains spaces your code will break: gunzip -c 'ens'"$line"'traj.pdb.gz' >> ... or: gunzip -c "ens${line}traj.pdb.gz" >> ... — Andreas Louv
– Andreas Louv, Commented Apr 25, 2016 at 20:45

Sir. Hedgehog · Accepted Answer · 2016-04-26 07:47:16Z

1

file="/home/input.txt"
grep -Po '/.*?/.*?/' $file > filenames.txt

structures='filenames.txt'
i=1
while IFS= read "line"
 do
   gunzip -c 'ens'$line'traj.pdb.gz' >> 'output'$i'.pdb'
   i=$(expr $i + 1)
 done <$structures

rm $structures

couple of logical mistakes, the counter has to be fined as one out of the while loop and the counter +1 should be inside the loop, also for the counter to work you have to use expr, in this case i made the counter start from 1, so the first entry will get this value. Also on the parameter for the while loop i dont really understand what you are doing, if it works as you have it then cool or else use a test statement after while and before the parameters.

edited Apr 26, 2016 at 7:47

answered Apr 26, 2016 at 7:30

Sir. Hedgehog

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7 Comments

tripleee Over a year ago

The temporary file and the spurious variables should be fixed as well. Simply grep -Po regex /home/input.txt | while IFS= read ...

tripleee Over a year ago

You cannot have a space before the equals sign in IFS=

tripleee Over a year ago

Also as already pointed out in comments, the silly quoting doesn't do anything useful, and the quotes are missing where they would be required (or at the very least useful).

Sir. Hedgehog Over a year ago

@tripleee does the while loop actually works with the parameters defined like this? cause depending on what he i checking there i think he needs the test thought

EA00 Over a year ago

@hedgehog - In the original code when I moved the counter inside the while loop and fixed the quotes, it seemed to work fine. But nonetheless I really appreciate all the input and as a beginner I can see how your code is more logically sound. Thanks!

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