#!/usr/bin/perl
#
# Parse simple FASTA text, chunk by chunk

use strict;
use warnings;

my $term = $/;
my $fastafile = 'fasta.txt';

my $pos = 0;
my $id;
my @sequencelines;
my $sequence;
my $line;

open(FASTA,"<",$fastafile) or die("Open failed: $!");

$/ = ">";
while(<FASTA>)
{
    chomp;

    # Since the file begins with ">", the first extraction will
    # contain only that '>', which will then get chomped, so we'll
    # have a blank line to skip.
    next if($_ eq '');

    ($id,@sequencelines) = split /\n/;

    # I'm not sure if the ID is supposed to include the '>' in front
    # of it or not, but if so, we can put it back.
    $id = '>' . $id;

    print "Found ID '",$id,"' at position ",$pos,":\n";

    $sequence = '';
    foreach $line (@sequencelines)
    {
        print $line,"\n";
        $sequence .= $line;
    }
    print "\n";
    $pos++;
}
$/ = $term;

##</code><code>##

Found ID '>ELKSMKO02JGD0L' at position 0:
TCAGGAATCTAATACTCAAGCTGTGGCCTATCCAGTACAACATGTAGCGAGACAATAATATCTCAGGATC
TGAATACACCCCTTCTGTTAAAATGCAGTCTAGGATTACACTAGCTTTGTTCACAGCCACGTAACACCAC
TGACTCACATGAAGACTGAAGACAACACAACCCCCCACATCTTGTTCACAAAAACTGGTAGCATGCCAGG
TCTTCCATATCTTTACAGGACACTTGGTATTTTACAAAACTTAATTC

Found ID '>ELKSMKO02FEYZW' at position 1:
TCAGTCATAATGTCATTTCTTCAAAACTTGATCTGTAGATTTAATGGAACCCCAATCAAAATTCCAGCAA
ATTATTAAGTGGATATCCACAAACTGGTTCAAAAGTTTATATGAAATAACAAAAGATCCAGAACAGCCAA
CATAATATTGAAGGAGAAGAATGAAGTTCGAGGTCTAACAAACTAATTTCTGTATGATTCCAACTACATG
GCATTCTGGAAAATGAAAAATTACAGACACAGTAAATAGCTCAGTGATTGCCAGGTAGG

Found ID '>ELKSMKO02IX3A4' at position 2:
TCAGTCCCAACGTGCTGGGAGGGCGTGAGCCACGGTGCCCAGCCTTTTTATTTTTTATTTTTATTTTTAA
TCTGTCTTGATTTTGCTTCCTTCCTAAACAGTTTTGGCTTCGTGATCACGTAAACCAAGAGTCACAAACT
GAAATGCCATCAAGGGGCCAAGCAGGTAACAAAATTCAAGTCATACAGGTTCAATGTCTTAGTCACCCCA
GGCTACAACAGAATATCATAGACTGGGTANCCTAATAATACAGATCATTTTCNCATGGTTCTAGAGGAC