root/bin/split_fasta

#! /usr/bin/perl -w

use strict "vars";
use strict "refs";

use FindBin;
use lib "$FindBin::Bin/../lib";
use vars qw($LOG $CMD_ARGS);

use Iterator::Fasta;

my $usage = "
Usage:

        split_fasta [count] <fasta_input>

        This script splits a multi-fasta file into the number of files specified by count.

";
#-----------------------------------------------------------------------------
#----------------------------------- MAIN ------------------------------------
#-----------------------------------------------------------------------------
if (@ARGV != 2){
    print $usage;
    exit;
}

#variables that are persistent outside of try block
my $count = shift @ARGV;
die "ERROR: the count nust be set to a value greater than 1.\n"if ($count <= 1);
my $infile = shift @ARGV;
die "ERROR: The file \'$infile\' does not exist.\n" if(! -e $infile);

my $fasta_iterator;
$fasta_iterator = new Iterator::Fasta($infile);

my @files;
my $i = 0;
while (my $fasta = $fasta_iterator->nextEntry()) {
    if(! defined($files[$i])){
        my $outfile = $infile;
        $outfile =~ s/\.fasta$//;
        $outfile .= "_part_$i.fasta";
        open(my $fh, "> $outfile");
        push(@files, $fh);
    }

    my $fh = $files[$i];

    print $fh $fasta ."\n";

    $i++;
    $i = 0 if ($i >= $count);
}

foreach my $fh (@files){
    close($fh);
}