#!/usr/bin/perl -w
# created by Jun Wang
# last modified: 10.16.06

use strict;
#use Data::Dumper;
#use Bio::SeqIO;
#use Bio::AlignIO;
#use DBI;

##############################
# make log file
#######################

my $directory;

for (my $i=0;$i<=$#ARGV;$i+=2){
	if($ARGV[$i] eq "-d"){
		$directory=$ARGV[$i+1];
	}
}

open (LOG,">>7blatAxtChain.log");
#open (STDERR,">8chainParse.err");
print LOG "\n".(localtime)."\n";
print LOG "chr_file:$directory\n";

if($directory eq ""){
	print "Usage: perl 7blatAxtChain.pl -d ortho_dir";
	exit(0);
}
########################
# grep the chr file from hg18 fold
#######################

opendir(DIR,$directory);
# `mkdir chain`;
#`chainMergeSort $directory/*.chain | chainSplit chain stdin`;

 
my @files_chr = grep{ /\.chain$/ && -f} map {"$directory/$_"} readdir(DIR);
closedir(DIR);


#`mkdir data/hg18/temp`; 
#`mkdir data/hg18/temp_orth`;
#`mkdir data/hg18/temp_orth_nib`;
#`mkdir data/hg18/axt1`;
#`mkdir data/hg18/chain1`;


for my $file_chr(@files_chr){

       $file_chr =~ m/(\S+)\/(\S+)\.chain$/;	

       my $query_chr = "$1";
       my $hit_chr = "$2";
       my $chain_name ="$1"."_"."$2";
       my $net_name = "$1"."_"."$2"."_"."net";
     # `mkdir $chain_name`;
     # `mkdir $net_name`;

       print "$chain_name\n";

       `~/bin/i386/chainMergeSort $file_chr | ~/bin/i386/chainSplit $chain_name stdin`;

############################
# read the file 
#########################
       opendir(DIR_chain,$chain_name);
       my @file_chain = grep{ /\.chain$/ && -f } map {"$chain_name/$_"} readdir(DIR_chain);
       closedir(DIR_chain);

		for my $file_chain(@file_chain){
		print "$file_chain\n";
		$file_chain =~ m/\/(\S+)\.chain$/;
		my $temp = $1;
		print "$temp\n";
		my $name_query = "$1"."_query.net";
		my $name_hit = "$1"."_hit.net";
		my $net_query = "$net_name/$name_query";
		my $net_hit = "$net_name/$name_hit";
	        my ($query_file,$target_file) = chr_size($net_name,$temp,$file_chain);
		`~/bin/i386/chainNet $file_chain $query_file $target_file $net_query $net_hit`;

		}

}


###########################
# read the size of chr
########################
sub chr_size {

	my ($net,$temp1,$file) = (@_); 
	
	open (INFILE,"<$file") || die "Fix the file\n";
	print "$file\n";
	print "enter\n";
	my $current_target="";
	my $current_query="";

	my $query_size = "$net"."/$temp1"."_"."query.size";
	my $target_size= "$net"."/$temp1"."_"."target.size";

	open(OUTquery,">$query_size");
	open(OUTtarget,">$target_size");

 
	while(<INFILE>){
		my $line = $_;
		chomp($line);
		if($line =~ /^chain/){
		my @line_info = split(/\s+/,"$line");

				my $current_target=$line_info[2];
				my @info = split(/_/,"$current_target");
				my $len = $info[$#info];
				print OUTtarget "$current_target\t","$len\n";
				print "$current_target\t","$len\n";

				

				my $current_query = $line_info[7];
				my @info1 = split(/_/,"$current_query");
				my $len1 = $info1[$#info1]-1;
				print OUTquery "$current_query\t","$len1\n";
				print "$current_query\t","$len1\n";

				


		}

	}

		return("$query_size","$target_size");	



}








exit(0);