cut -d " " -f 1 sequences.fa | tr -s "\n" "\t"| sed -s 's/>/\n/g' > sequences.tabwhile read id start end; do \g=$(grep "$id" sequences.tab | cut -f 2 | cut -c $start-$end);\echo ">$id";\echo $g;\done

#!/usr/bin/perl -wuse Bio::DB::Fasta;#Usage: extract_substring.pl file.fasta coordinates.txt (where: id, start, stop) > out.fastamy $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 (
    
     ) {    ($id,$start,$stop) = split "\t";    my $subseq = $db->subseq($id,$start,$stop);    print ">", $id, "_", $start, "_", $stop;     print $subseq, "\n";  }close IN1;