Process a fasta format file and provide output based on http://stackoverflow.com/questions/33131723/how-to-get-each-fasta-sequence-in-one-line-with-its-id-when-multiple-sequences-a

custom_fasta_proc.pl

#!/usr/bin/perl

use strict;
use warnings;

use Data::Dumper;

die "Usage: $0 FASTA_FILE" if !$ARGV[0];

# read the fasta file
my @lines;
open(FH, $ARGV[0]);
chomp(@lines = <FH>);
close(FH);

# output updates
my $curr_id;
my $curr_seq;
foreach my $l (@lines) {
    # the regex below can be updated along with the logic
    # the regex list of possible codes in a seq can be expanded based on https://en.wikipedia.org/wiki/FASTA_format
    # or can match ids if it will always follow a particular format
    if($l =~ m{^[ACGTU]+$}) {
        $curr_seq .= $l; 
    }   
    else {
        print "$curr_id\n$curr_seq\n" if ($curr_id && $curr_seq); # at this point we have an id and the entire seq to go with that id
        $curr_id = $l; 
        $curr_seq = ""; 
    }   
}

print "$curr_id\n$curr_seq\n" if ($curr_id && $curr_seq); # last one