1

I have a file input.txt with three columns

A B Z
C D Y
E F X

I want to read the first two fields, perform some function and name the output with the last field.

while IFS=" " read -r f1 f2 f3; do cat $f1 $f2 > $f3; done < file.txt

How can I apply this to longer codes

the input.sample.text has following three columns

../Data/G20P1sc-C05-R1.fastq.gz ../Data/G20P1sc-C05-R1.fastq.gz G20P1sc-C05
../Data/G20P1sc-C08-R1.fastq.gz ../Data/G20P1sc-C08-R1.fastq.gz G20P1sc-C08
 while IFS=" " read -r f1 f2 f3; do rsem-calculate-expression --star --star-path /share/pkg/star/2.7.0e/bin --temporary-folder --star-gzipped-read-file --paired-end $f1 $f2 ../genome_indices/rsem-star/rsem-star ../test_results/$f3; done < src_pdm3012/input.sample.text 

The output has the following error

EXITING: FATAL INPUT ERROR: empty value for parameter "outFileNamePrefix" in input "Command-Line-Initial"
SOLUTION: use non-empty value for this parameter

I try to explicitly use the --outFileNamePrefix and it still has the same error

while IFS=" " read -r f1 f2 f3; do rsem-calculate-expression --star --star-path /share/pkg/star/2.7.0e/bin --temporary-folder --star-gzipped-read-file --paired-end $f1 $f2 ../genome_indices/rsem-star/rsem-star --outFileNamePrefix $f3; done < ../src_pdm3012/input.sample.text
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  • 2
    What is your question exactly? – Sparhawk May 30 '19 at 22:44
  • 1
    What do you mean by "longer codes"? – Kusalananda May 30 '19 at 22:44
  • I was hoping I could apply this to mapping multiple fastq files and naming the output. – PDM May 30 '19 at 22:45
  • Something Like this: while IFS=" " read -r f1 f2 f3; do rsem-calculate-expression --star --star-path /share/pkg/star/2.7.0e/bin --temporary-folder --star-gzipped-read-file --paired-end $f1 $f2 ../genome_indices/rsem-star/rsem-star --outFileNamePrefix $f3; done < ../src_pdm3012/input.sample.text But it does not work – PDM May 30 '19 at 22:46
  • 3
    How does it "not work"? What are the error messages? I'd suggest editing your question and putting this very relevant information in it. – Sparhawk May 30 '19 at 22:49
2

I suggest awk script to do this:

awk '{ print $1,$2 > $3}'

Of course you must be sure that $3 exists (and is unique) and that there is no confution what the third column is, i.e. columns 1, 2, and 3 should not contain field separators.

awk will also allow you manyfold manipulations on the first two columns.

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  • It's not clear what this does that the code in the question does not do. – Kusalananda May 31 '19 at 9:04
  • @Kusalananda "longer codes" and "perform some function" in the question is a bit unspecific. It could well be a problem fitting for awk with this answer just showing how to get a column as per-line filename for the output. – FelixJN May 31 '19 at 9:26
  • this code write line field $1 and line field $2 into output file named by line field $3 – Dudi Boy May 31 '19 at 19:55
0

You can redirect a command group or any form of compound command to redirect the output of more than one command, whether it's a while loop or not:

while IFS=" " read -r f1 f2 f3; do
  {
    cat < "$f1"
    echo whatever
    cat < "$f2"
    echo end
  } > "$f3"
done < file.txt

Also remember that in POSIX shells, variables expansions need to be quoted.

1
  • @Stéphan..can you show how to write the above code for rsem-calculate-expression in while loop ? I guess, the difference from your answer in format is , in my code the output will be within the brackets. – PDM May 31 '19 at 14:31

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