I have a file which has two file names per row, like this:
file1.fastq.gz file2.fastq.gz
...
file9fastq.ga file10fastq.gz
How can I pass the two names as arguments for a script?
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Each **line** of the input file should be use as parameters to the script? – RonJohn Jul 26 '19 at 02:22
2 Answers
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Using a while read loop:
while read -r file1 file2 trash; do
something with "$file1" and "$file2"
done < /path/to/input_file
This will read your input file line by line, setting file1 and file2 with the first and second columns respectively. trash is probably unnecessary but I like to include it to handle things you may encounter such as:
file1.fastq.gz file2.fastq.gz foo
If your file contained a line like the above and you did not include the trash variable (or one similar), your file2 variable would be set to: file2.fastq.gz foo
Kusalananda
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jesse_b
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I tried `while read -r file1 file2 trash; do BatchTester $file1 $file2 done < configseparated` but instead of executing it what I get is space too keep writing instead of execution however the sheel then only o gives me the opportunity to keep writing – The69Er Jul 30 '19 at 17:45
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xargs is another way, if your file format is exactly as you say: two whitespace-separated fields per line (noting the ... ellipsis).
< input xargs -n2 ./script-here
... will read the file named input line-by-line and pass two arguments to ./script-here.
You can rearrange the redirection:
xargs -n2 ./script-here < input
... if it makes better intuitive sense to you.
Jeff Schaller
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