automate command using bash or perl script?

Question

[sharmatina189059]

Dear all I have a file containing genome Ids like

470.771
470.773

......so on upto 1000

and I need to automate a command for all 1000 genome id. Command is

p3-genome-fasta --contig 470.771 > out.contig

and I need a folder containing all the downloaded files. Can anybody help me out with this task?

[cpad0112]

try this and let me know if this is what you want:

$ parallel --dry-run  'p3-genome-fasta --contig {} > out_{}.contig' ::: 470.{771..1000}

if you have the ids in text file (ids.txt), try this:

$ parallel --dry-run  'p3-genome-fasta --contig {} > out_{}.contig' :::: ids.txt

remove dry-run to execute the command.

Answer 1

[ATpoint]

for i in 470.{771..1000}
  do 
  p3-genome-fasta --contig ${i} > out_${i}.contig
  done

What do you mean by "a folder"? What does this command produce?

Answer 2

[JC]

Not sure if your output need to be renamed, but here is in Perl:

#!/usr/bin/perl
use strict;
use warnings;

while (<>) {
    chomp;
    my $id = $_;
    system("p3-genome-fasta --contig $id > out_$id.contig")
}

so you can run as perl run.pl < file_with_ids.txt

[sharmatina189059]

Thanks for replying.. It works.