cut -d " " -f 1 sequences.fa | tr -s "\n" "\t"| sed -s 's/>/\n/g' > sequences.tab

while read id start end; do \

g=$(grep "$id" sequences.tab | cut -f 2 | cut -c $start-$end);\

echo ">$id";\

echo $g;\

done<coordinates.txt

#!/usr/bin/perl -w

use Bio::DB::Fasta;

#Usage: extract_substring.pl file.fasta coordinates.txt (where: id, start, stop) > out.fasta

my $fasta = $ARGV[0];

my $query = $ARGV[1];

my ($id,$start,$stop);

my $db = Bio::DB::Fasta -> new($fasta);   # Create database from a directory of Fasta files

                                          # my $db       = Bio::DB::Fasta->new('/path/to/fasta/files/');

open (IN1, $query);

  while (<IN1>) {

    ($id,$start,$stop) = split "\t";

    my $subseq = $db->subseq($id,$start,$stop);

    print ">", $id, "_", $start, "_", $stop;

    print $subseq, "\n";

  }

close IN1;

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