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#!/usr/bin/perl -w
#Filename:
#Author: Tian Dongmei
#Email: [e-mail]
#Date: 2013/7/19
#Modified:
#Description: 
my $version=1.00;

use strict;
use Getopt::Long;
use File::Basename;

my %opts;
GetOptions(\%opts,"i=s","ref=s","index:s","v:i","p:i","o=s","h");
if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
&usage;
}

my $filein=$opts{'i'};
my $fileout=$opts{'o'};
unless ($fileout=~/\/$/) {$fileout.="/";}
my $rfam=$opts{'ref'};
my $mis=defined $opts{'v'}? $opts{'v'} : 0;
my $index=defined $opts{'index'} ? $opts{'index'} : "";
my $threads=defined $opts{'p'} ? $opts{'p'} : 1;


#my $time=time();

#my $mapdir=$fileout."/rfam_match_".$time;
my $mapdir=$fileout."/rfam_match";
mkdir $mapdir;
chdir $mapdir;
###check genome index
if (-s $index.".1.ebwt") {
}else{
	&checkACGT($rfam);
	`bowtie-build $rfam rfam`;
	$index="rfam";
}

#chdir "rfam_match_1397022331";
### genome mapping
`bowtie -v $mis -f -p $threads -k 1 $index $filein --al rfam_mapped.fa --un rfam_not_mapped.fa > rfam_mapped.bwt`;

sub checkACGT{
	my $string;
	open IN,"<$rfam";
	while (my $aline=<IN>) {
		if ($aline!~/^>/) {
			$aline=~s/U/T/gi;
		}
		$string .=$aline;	
	}
	close IN;
	$rfam=basename($rfam);
	open OUT, ">$rfam";
	print OUT $string;
	close OUT;
}

sub usage{
print <<"USAGE";
Version $version
Usage:
$0 -i -o
options:
-i input file# input reads fasta/fastq file
-ref input file# rfam file, which do not contain miRNAs
-index file-prefix #(must be indexed by bowtie-build) The parameter
                string must be the prefix of the bowtie index. For instance, if
                the first indexed file is called 'h_sapiens_37_asm.1.ebwt' then
                the prefix is 'h_sapiens_37_asm'.##can be null
-v <int>           report end-to-end hits w/ <=v mismatches; ignore qualities,default 0;

-p/--threads <int> number of alignment threads to launch (default: 1)

-o output directory 

-h help
USAGE
exit(1);
}