How to use gnu in parallel on a range of numbers given by command line arguments
I am trying to use gnu in parallel with some basic bioinformatics tools like. lastz. That is to say, I have 10 seconds and I want to use lastz for all of them, I use:
parallel --dryrun lastz 'pathToFile/seq{}.fa query.fasta --format=text > LASTZ_results_seq{}' ::: {1..10}
Which works fine and returns:
lastz pathToFile/seq1.fa query.fasta --format=text > LASTZ_results_seq1
lastz pathToFile/seq2.fa query.fasta --format=text > LASTZ_results_seq2
lastz pathToFile/seq3.fa query.fasta --format=text > LASTZ_results_seq3
...
lastz pathToFile/seq10.fa query.fasta --format=text > LASTZ_results_seq10
But ideally I would like this step to be part of a bash script that takes three command line arguments, so the number of sections (for example, 1 to 10) is given on the command line (with $ 2 = startValue, $ 3 = endValue). I thought I would change it to this:
parallel --dryrun lastz 'pathToFile/seq{}.fa query.fasta --format=text > LASTZ_results_seq{}' ::: {"$2".."$3"}
but returns instead
lastz pathToFile//seq\{\1..\10\} query.fasta --format=text > LASTZ_results_seq\{\1..\10\}
Can someone please tell me what I am doing wrong here? It looks like it interprets $ 2 as 1 and $ 3 as 10, but then cannot treat it as a range of numbers ...
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This is not what you are asking, but this might be a better solution:
parallel --dryrun lastz {} query.fasta --format=text '>' LASTZ_results_{/.} ::: pathToFile/seq*.fa
If you get Argument list too long
try:
printf '%s\n' pathToFile/seq*.fa | parallel --dryrun lastz {} query.fasta --format=text '>' LASTZ_results_{/.}
This way you don't need to know in advance how many seq * .fa there are.
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Bash ranges don't accept variables, see this post:
How do I iterate over a range of numbers defined by variables in Bash?
thus I suggest you change {$ 1 .. $ 2} to $ (seq $ 1 $ 2).
For example see this test script:
$ cat foo
parallel echo ::: {1..3}
parallel echo ::: {$1..$2}
parallel echo ::: $(seq $1 $2)
when called as. / foo 1 3, it produces the following output:
1 2 3 {1..3} 1 2 3
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