Using Bash script to run multiple files through java code

Question

I have some code that is used to analyse files, the code is setup to analyse 1 file at a time using the following command line input in the /home/john/Dropbox/PhD/MultiFOLDIA/ directory:

java MultiFOLDIA_IMODE1 complex.1.pdb /home/john/Dropbox/PhD/MultiFOLDIA/Poses/ T0868_T0869 /home/john/Dropbox/PhD/MultiFOLDIA/T0868_T0869_complex.1.pdb_IMODE1.txt > /home/john/Dropbox/PhD/MultiFOLDIA/MultiFOLDIA_IMODE1.log

I would like to run the command on every file in the /home/john/Dropbox/PhD/MultiFOLDIA/Poses/ directory and have tried using the following script:

#!/bin/bash

poses=(~/home/john/Dropbox/PhD/MultiFOLDIA/Poses/*)

for f in "${poses[@]}"; do
java MultiFOLDIA_IMODE1 "$f" /home/john/Dropbox/PhD/MultiFOLDIA/Poses/ T0868_T0869 /home/john/Dropbox/PhD/MultiFOLDIA/T0868_T0869_"$f"_IMODE1.txt > /home/john/Dropbox/PhD/MultiFOLDIA/MultiFOLDIA_IMODE1.log
done

It doesn't work and I think I am not understanding how to pull filenames from arrays and utilise them in this way.

Eric Duminil · Accepted Answer · 2016-11-24 22:13:07Z

1

~/ is already /home/john.

So ~/home/john probably doesn't exist.

This should bring you closer to your goal :

cd /home/john/Dropbox/PhD/MultiFOLDIA/Poses/

for pdb in *.pdb
do
  echo "Processing $pdb"
  java MultiFOLDIA_IMODE1 "$pdb" ./ T0868_T0869 ../T0868_T0869_"$pdb"_IMODE1.txt >> ../MultiFOLDIA_IMODE1.log
done

edited Nov 24, 2016 at 22:13

answered Nov 24, 2016 at 22:00

Eric Duminil

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2 Comments

Johnny Over a year ago

Hurrah this worked, now to educate myself as to why it works ;) Thank you Eric

Eric Duminil Over a year ago

Is there something you don't understand in particular?

pato · Accepted Answer · 2016-11-24 22:34:11Z

1

This should work.

find /home/john/Dropbox/PhD/MultiFOLDIA/Poses/ -maxdepth 1 -type f -exec java MultiFOLDIA_IMODE1 '{}' /home/john/Dropbox/PhD/MultiFOLDIA/Poses/ T0868_T0869 /home/john/Dropbox/PhD/MultiFOLDIA/T0868_T0869_'{}'_IMODE1.txt >> /home/john/Dropbox/PhD/MultiFOLDIA/MultiFOLDIA_IMODE1.log \;

Also, when redirecting output use >> instead of >. > truncate file and in the end you will have only logs from last execution eg:

$ echo a > test.txt
$ echo a > test.txt
$ cat test.txt
a

$ echo a >> test.txt
$ echo a >> test.txt
$ cat test.txt
a
a

edited Nov 24, 2016 at 22:34

answered Nov 24, 2016 at 22:03

pato

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3 Comments

Eric Duminil Over a year ago

This won't work like this. You should remove -path and you're trying to use an undefined "$f".

pato Over a year ago

True that, I missed this "$f"

Johnny Over a year ago

Thanks for the tip about redirecting output, very useful.

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