ds_data_extractor_new_parser

#!/usr/bin/perl -w 
use strict;
use lib ('/home/mcampbell/lib');

#use Getopt::Std;
#use vars qw($opt_t);
#getopts('t:');

use PostData;

$| = 1;

use Bio::SearchIO;
use FileHandle;


my $usage = "

USAGE: ds_data_extractor_new_parser <master org> <target org 1> <target org 2> <outfile 1> <outfile 2> 

\n"; 

#-----------------------------------------------------------------------------
#----------------------------------- MAIN ------------------------------------
#-----------------------------------------------------------------------------


my %DATA;
my %STR;
my %BAD;


die $usage unless $ARGV[2];

my $M = shift @ARGV;
my $A = shift @ARGV;
my $B = shift @ARGV;

my $i = 0;

while (defined(my $file = shift @ARGV)){

	parse($file, $i);

	$i++;
}

#set_maxo();

#PostData(\%DATA);

foreach my $id (keys %DATA){
	next if is_bad($id); # i.e. not present in all input files.
 

	foreach my $o (sort {$a <=> $b} keys %{$DATA{$id}}){
		my $mn;
		my $an;
		my $bn;
		if     (exists($DATA{$id}{$o}{$A}) && exists($DATA{$id}{$o}{$B})){
			# $A & $B
			$mn = $DATA{$id}{$o}{$A}->{q};
			$an = $DATA{$id}{$o}{$A}->{s};
			$bn = $DATA{$id}{$o}{$B}->{s};
			
			my $x = $DATA{$id}{$o}{$A}->{q};
			my $y = $DATA{$id}{$o}{$B}->{q};

			die "Q NUC NOT SAME!\n" unless $x eq $y;

		}
		elsif (exists($DATA{$id}{$o}{$A})){
			# $A only
			$mn = $DATA{$id}{$o}{$A}->{q};
			$an = $DATA{$id}{$o}{$A}->{s};
			$bn = '-';
		}
		elsif (exists($DATA{$id}{$o}{$B})){
			# $B only
			$mn = $DATA{$id}{$o}{$B}->{q};
			$an = '-';
			$bn = $DATA{$id}{$o}{$B}->{s};
			
		}

                $STR{$id}{M} .= $mn;
                $STR{$id}{A} .= $an;
                $STR{$id}{B} .= $bn;

	}
}

spew();

#-----------------------------------------------------------------------------
#---------------------------------- SUBS -------------------------------------
#-----------------------------------------------------------------------------
sub is_bad {

	my $id = shift;

	my @keys = keys %{$BAD{$id}};
	return 1 if @keys < 2;
	return 0;
}
#-----------------------------------------------------------------------------
sub spew {

	foreach my $id (keys %STR){
		print ">$id\n";
		for (my $i = 0; $i < length($STR{$id}{M}); $i +=60){
			print substr($M, 0, 5)." ".substr($STR{$id}{M}, $i, 60)."\n";
			print substr($A, 0, 5)." ".substr($STR{$id}{A}, $i, 60)."\n";
			print substr($B, 0, 5)." ".substr($STR{$id}{B}, $i, 60)."\n";
			print "\n";
		}
		#print "\n";
	}
}
#-----------------------------------------------------------------------------
sub parse {
	my $file = shift;
	my $i    = shift;

	my $fh = new FileHandle();
	   $fh->open($file);

	while (defined(my $line = <$fh>)){
		chomp($line);

		my @stuff = split(/\t/, $line);

		$BAD{$stuff[2]}{$i}++;

		$DATA{$stuff[2]}{$stuff[3]}{$stuff[1]} = 
		{q => $stuff[4], s => $stuff[5]};

	}


	$fh->close();

}
#-----------------------------------------------------------------------------