for loop with multiple commands

Question

I have multiple filenames in files.txt. I want to run three scripts on each file. I my suggestion correct?

files.txt:

SRR13143.sra
SRR44234.sra
SRR23424.sra

my try:

for FILE in "file.txt";
do
prefetch --max-size 300G $FILE
fastq-dump --gzip --split-3 $FILE
rm $FILE;
done

You're not reading filenames from `file.txt`, you're just looping over the name `file.txt` literally. — Barmar, Jan 30 '19 at 18:17
BTW, you should always quote variables unless you have a good reason not to. — Barmar, Jan 30 '19 at 18:17

score 2 · Accepted Answer · answered Jan 30 '19 at 18:16

2

You want a while loop instead.

while IFS= read -r FILE; do
  prefetch --max-size 300G "$FILE"
  fastq-dump --gzip --split-3 "$FILE"
  rm "$FILE"
done < file.txt

answered Jan 30 '19 at 18:16

chepner

1

Maybe as a finishing touch, prefer lower case for your private variable. – tripleee Jan 30 '19 at 18:40
1

Might want to redirect the commands in the loop ` – Charles Duffy Jan 30 '19 at 18:40
If one of the script adds a extenstion to the output, for instance SRR13143.sra.gz, could I write: "$FILE".gz ?? – user2300940 Jan 30 '19 at 18:58

1 Answers1