#!/usr/bin/env perl
# fasta_flattener.pl
# Mike Covington
# created: 2012-06-14
#
# Description: flatten a FASTA file by removing white space
#
use strict;
use warnings;
use Bio::SeqIO;
use v5.10; #or later... or change 'say' to 'print' X_x

my $fasta_in = "input.fa";
open my $fasta_out, ">", "output.fa";

my $seqio_in = Bio::SeqIO->new(
    -file   => $fasta_in,
    -format => 'Fasta',
);

my ( $seq_obj, %seq_hash );

while ( my $seq_obj = $seqio_in->next_seq() ) {
    my $seq_id = $seq_obj->display_id();    #this is the sequence ID
    my $seq    = $seq_obj->seq();           #this is the actual sequence
    $seq_hash{$seq_id} = $seq;              #and hashed!

    #to print them to your screen in a "consolidated" FASTA format:
    say ">$seq_id";
    say $seq_hash{$seq_id};

    #to save to a file in a "consolidated" FASTA format:
    say $fasta_out ">$seq_id";
    say $fasta_out $seq_hash{$seq_id};
}
exit;