Hello abcd,

The following demonstration uses the BioUtil::Seq module on CPAN. It is beneficial for this use case.

use strict;
use warnings;

use BioUtil::Seq;
use constant { HDR => 0, SEQ => 1 };

# From the documentation:
#
# FastaReader returns an anonymous subroutine, when called, returns
# a fasta record which is a reference of an array containing the fasta
# header and sequence. By default, spaces and \r?\n are trimmed from
# the sequence.
#

my $next_seq = FastaReader("input_file.fasta");

while ( my $fa = $next_seq->() ) {
 # print ">$fa->[HDR]\n$fa->[SEQ]\n";
   my $name = ( split(/ /, $fa->[HDR], 2) )[0];

   while ( $fa->[SEQ] =~ /(?<=(.....))abc(.{10})def(?=(.....))/g ) {
      print "$name: $1, $2, $3\n";
   }
}

[download]

Regards, Mario.

In reply to Re: Regular expressions across multiple lines by marioroy
in thread Regular expressions across multiple lines by abcd

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