A one loop solution that uses regexen to find the positions of all starters and stoppers then, in a loop over starters, uses List::Util::first() to find the next stopper that fits the criteria.

use strict;
use warnings;

use 5.018;
use List::Util qw{ first };

open my $fastaFH, q{<}, \ <<EOD or die $!;
>NC_001422.1 Enterobacteria phage phiX174 sensu lato, complete genome
GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG
TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
EOD
chomp( my @seqLines = <$fastaFH> );
close $fastaFH or die $!;

my $sequence = join q{}, @seqLines[ 1 .. $#seqLines ];

my @starts;
push @starts, pos $sequence
   while $sequence =~ m{(?=ATG)}g;

my @stops;
push @stops, pos $sequence
   while $sequence =~ m{(?=(?:TAG|TAA|TGA))}g;

foreach my $start ( @starts )
{
    my $firstStop =
       first {
           $_ > ( $start + 3 )
           and not
           ( ( $_ - $start ) % 3 )
       } @stops;

    next unless $firstStop;
    say qq{ORF: $start - $firstStop};

    shift @stops while $stops[ 0 ] < $start;
}

[download]

The output:

ORF: 16 - 133
ORF: 50 - 218
ORF: 132 - 390
ORF: 229 - 328
ORF: 249 - 390
ORF: 283 - 328
ORF: 301 - 328
ORF: 358 - 373
ORF: 389 - 845
ORF: 483 - 498
ORF: 567 - 840
ORF: 642 - 840
ORF: 680 - 845
ORF: 714 - 840
ORF: 842 - 944
ORF: 847 - 961
ORF: 941 - 1193
ORF: 1037 - 1193
ORF: 1211 - 1256
ORF: 1232 - 1256

[download]

I hope this is of interest.

Cheers,

JohnGG

In reply to Re: finding open reading frames by johngg
in thread finding open reading frames by ic23oluk

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