for loop with multiple commands [duplicate]

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
– Barmar, Commented Jan 30, 2019 at 18:17
BTW, you should always quote variables unless you have a good reason not to. — Barmar
– Barmar, Commented Jan 30, 2019 at 18:17

chepner · Accepted Answer · 2019-01-30 18:16:13Z

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, 2019 at 18:16

chepner

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3 Comments

tripleee Over a year ago

Maybe as a finishing touch, prefer lower case for your private variable.

Charles Duffy Over a year ago

Might want to redirect the commands in the loop </dev/null if we don't know them not to consume stdin, just out of caution. Or put file.txt on an alternate fd.

user2300940 Over a year ago

If one of the script adds a extenstion to the output, for instance SRR13143.sra.gz, could I write: "$FILE".gz ??

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