#!/usr/bin/perl -w


#### DEBUG


#### TIME

my $time = time();




my $delay = 30;

print "Sleeping $delay seconds...\n";

sleep($delay);



=head2


	APPLICATION     splitace




        **** DUMMY EXECUTABLE TO TEST WORKFLOW ****




    PURPOSE


        1. SPLIT A LARGE .ace FILE INTO SMALLER .ace FILES FOR EACH CONTIG


        2. WRITE THE INDIVIDUAL CONTIG .ace FILE IN NUMBERED SUBDIRECTORIES


            BASED ON THE NUMBER OF THE CONTIG (E.G., THE .ace FILES FOR CONTIGS


            1 TO 100 GO IN SUBDIRECTORY '100', THE .ace FILES FOR CONTIGS


            701-800 GO IN SUBDIRECTORY '800', ETC.)


    INPUT


        1. AN .ace FILE


    OUTPUT


        1. MULTIPLE .ace FILES - ONE FOR EACH CONTIG IN THE INPUT .ace FILE


    USAGE


    ./splitace.pl <-i inputfile> [-h]


    -i inputfile            :   /full/path/to/inputfile

    -i outputdir     :   /full/path/to/outputdir

    -h help                 :   print help info


    EXAMPLES


./splitace.pl -i /home/syoung/base/pipeline/run2-lane6-mtdna-velvet/data/s_6_1_sequence.ace -o /home/syoung/base/pipeline/run2-lane6-mtdna-velvet/assembly/acefiles


=cut


use strict;


#### USE LIBRARY

use FindBin qw($Bin);

use lib "$Bin/../../../lib";


#### INTERNAL MODULES

use Timer;

use Util;
use Conf::Agua;


#### EXTERNAL MODULES

use Term::ANSIColor qw(:constants);

use Data::Dumper;

use Getopt::Long;


my @arguments = @ARGV;



#### GET OPTIONS

my $inputfile;

my $outputdir;

my $help;

if ( not GetOptions (

    'inputfile=s' => \$inputfile,

    'outputdir=s' => \$outputdir,

    'help' => \$help

) )

{ print "Use option --help for usage instructions.\n";  exit;    };


#### PRINT HELP

if ( defined $help )	{	usage();	}


print "Inputfile: $inputfile\n";

print "Outputdir: $outputdir\n";


#### CHECK INPUTFILE

if ( not defined $inputfile )

{

    print "Input file not defined (option --inputfile)\n";

    usage();

}

if ( not -f $inputfile )

{

    die "Could not find input file: $inputfile\n";

    usage();

}



#### CHECK OUTPUT DIRECTORY

if ( not defined $outputdir )    {    print "Output directory not defined (option --outputdir)\n"; usage();	}

if ( not -d $outputdir )

{

    mkdir($outputdir) or die "Can't make directory: $outputdir\n";

    if ( not -d $outputdir )

    {

        die "Could not create output directory: $outputdir\n";

    }

}


#### OPEN INPUT FILE

open(FILE, $inputfile) or die "Can't open input file: $inputfile\n";


#### SET RECORD DIVIDER

$/ = "\nCO ";


#### CHECK FIRST LINE TO MAKE SURE ITS AN .ace FILE 

my $line = <FILE>;

if ( $line !~ /^AS\s+\d+\s+\d+\s*$/ms )

{

    die "Input file does not have .ace-format ('AS <no. contigs> <no. bases>') first line: $line";

}


while ( <FILE> )

{


    my ($contig_number, $number_reads, $contig_length) = $_ =~ /^(\S+)\s+(\d+)\s+(\d+)/i;


	#### REMOVE ANY INFO AFTER THE FIRST "|" BAR IN THE CONTIG NUMBER

	$contig_number =~ s/\|.+$//;


	#### REMOVE ANY LEADING NON-NUMERIC SYMBOLS IN CONTIG NUMBER

	$contig_number =~ s/^(\D+)//;


    my $output_subdir = int($contig_number / 100) + 1;


    $output_subdir = $output_subdir . "00";

    if ( not $output_subdir )

    {

        $output_subdir = "000";

    }


    print "Output subdir: $output_subdir\n";

    my $output_dirpath = "$outputdir/$output_subdir";

    print "output_dirpath: $output_dirpath\n";


    if ( not -d $output_dirpath )

    {

        mkdir($output_dirpath) or die "Can't create directory: $output_dirpath\n";

        if ( not -d $output_dirpath )

        {

            die "Could not create output subdirectory: $output_dirpath";

        }

    }


	if ( $^O =~ /^MSWin32$/ )   {   $output_dirpath =~ s/\//\\/g;  }


    print "output_dirpath: $output_dirpath\n";



    #### SET OUTPUT FILE

    my $outputfile = "$output_dirpath/contig.$contig_number.ace";

	if ( $^O =~ /^MSWin32$/ )   {   $outputfile =~ s/\//\\/g;  }

    print "Outputfile: $outputfile\n";



    #### REMOVE ENDING 'CO' FROM OUTPUT

    $_ =~ s/CO\s*$//;


    #### OPEN OUTPUT FILE

    open(OUTFILE, ">$outputfile") or die "Can't open output file: $outputfile\n";

    print OUTFILE "AS $number_reads $contig_length\n\n";

    print OUTFILE "CO Contig";

    print OUTFILE $_;

    close(OUTFILE);

    #`cat $outputfile`;

}



#### PRINT RUN TIME

my $runtime = Timer::runtime( $time, time() );

print "Run time: $runtime\n";

print "Completed $0\n";

print Util::datetime(), "\n";

print "****************************************\n\n\n";

exit;


#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

#									SUBROUTINES

#:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::



sub usage

{

	print GREEN <<"EOF";


	APPLICATION     splitace




        **** DUMMY EXECUTABLE TO TEST WORKFLOW ****




    PURPOSE


        1. SPLIT A LARGE .ace FILE INTO SMALLER .ace FILES FOR EACH CONTIG


        2. WRITE THE INDIVIDUAL CONTIG .ace FILE IN NUMBERED SUBDIRECTORIES


            BASED ON THE NUMBER OF THE CONTIG (E.G., THE .ace FILES FOR CONTIGS


            1 TO 100 GO IN SUBDIRECTORY '100', THE .ace FILES FOR CONTIGS


            701-800 GO IN SUBDIRECTORY '800', ETC.)


    INPUT


        1. AN .ace FILE


    OUTPUT


        1. MULTIPLE .ace FILES - ONE FOR EACH CONTIG IN THE INPUT .ace FILE


    USAGE


    ./splitace.pl <-i inputfile> [-h]


    -i inputfile            :   /full/path/to/inputfile

    -i outputdir     :   /full/path/to/outputdir

    -h help                 :   print help info


    EXAMPLES


./splitace.pl -i /home/syoung/base/pipeline/run2-lane6-mtdna-velvet/data/s_6_1_sequence.ace -o /home/syoung/base/pipeline/run2-lane6-mtdna-velvet/assembly/acefiles


=cut


EOF


	print RESET;


	exit(1);

}