#!/Users/distiller/project/miniconda/conda-bld/augustus_1629408187913/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/bin/perl 
#
# splitMfasta.pl
# split a multiple fasta file in smaller multiple fasta files
# 
# This script is used by the braker.pl pipeline.
# Please be extremely careful when changing this script because the braker.pl
# pipeline may fail upon custom modification of this script.
# In case of doubt, contact katharina.hoff@uni-greifswald.de 
# 
# Mario Stanke, 2.04.2007, last modification by Katharina J. Hoff on Feb 21st 2018
#
#

use strict;
use Getopt::Long;
use File::Basename qw(basename);
use File::Spec::Functions qw(rel2abs);

my $usage = "$0 -- split a multiple fasta file in smaller multiple fasta files.\n\n";
$usage .= "Usage: $0 input.fa\n\n";
$usage .= "parameters:\n";
$usage .= "--minsize=n       each split output fasta file total to at least this man base pairs.\n";
$usage .= "                  set this to 0 to split the input in single sequence files.\n";
$usage .= "--outputpath=s    prefix to output path. Output files are\n";
$usage .= "                  s/input.split.1.fa\n";
$usage .= "                  s/input.split.2.fa\n";
$usage .= "                  s/input.split.3.fa\n";
$usage .= "                  ... \n";
$usage .= "\n";



if (@ARGV < 1) {
    print $usage;
    exit;
}

my ($seqfilename, $minsize, $outputpath,$cursize, $idx, $basename);
my $minsize = 0;
my $outputpath = "";

GetOptions('minsize:i'=>\$minsize,
	   'outputpath:s'=>\$outputpath);

$seqfilename = $ARGV[0];
if($outputpath =~ /^~/){
    my $HOME = $ENV{'HOME'};
    $outputpath=~s/~/$HOME/;
}
 
$outputpath=rel2abs($outputpath);
if ($outputpath ne "" && $outputpath !~ /\/$/){
    $outputpath .= "/";
}

open(SEQ, "<$seqfilename") or die ("Could not open $seqfilename");

$idx=0;
$cursize=0;
my $basename = basename($seqfilename);
$basename =~ s/(\.fa|\.fna|\.fasta)$//;

while (<SEQ>) {
    if ($idx == 0 || $cursize > $minsize && /^>/){
	$idx++;
	if ($idx > 1) {
	    close(SPLIT);
	}
	open (SPLIT, ">$outputpath$basename.split.$idx.fa") or die ("Could not open $basename.split.$idx.fa");
	$cursize = 0;
    }
    print SPLIT;
    if (!/^>/) {
	$cursize += (length $_) - 1;
    }
}
