annotate_admire.pl

=head1 LICENSE
Copyright [2017] [Ninad Oak]										
													
Licensed under the Apache License, Version 2.0 (the "License");						
you may not use this file except in compliance with the License.					
You may obtain a copy of the License at									
													
    http://www.apache.org/licenses/LICENSE-2.0								
													
Unless required by applicable law or agreed to in writing, software					
distributed under the License is distributed on an "AS IS" BASIS,					
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.				
See the License for the specific language governing permissions and					
limitations under the License.										

=cut

=head2 USAGE

## Step-by-step Guide:
(1) Download the github repository nroak/ADmiRE/annotate_tsv_using_perl/

(2) cd /annotate_tsv_using_perl

(3) gzip -d ADmiRE.tab.gz

(4) perl annotate_admire.pl [--input INPUT_FILE] [--output OUTPUT_FILE] [--admire_path=PATH] [--chr=NUMBER] [--pos=NUMBER]

# Detailed desription of the input options:

--input: INPUT_FILE

--output: OUTPUT_FILE (Default: INPUT_FILE.ADmiRE.tab)

--admire_path: Path to ADmiRE.tab database. (Default: same directory with annotate_admire.pl)

--chr: Column number in the INPUT_FILE with chromosome information. (Default: 1 -1st column)

--pos: Column number in the INPUT_FILE with base position information. (Default: 2 -2nd column)

=cut

=head1 HEADERS
ADmiRE Headers												
     1  Chromosome
     2  Start
     3  Stop
     4  MIRNA
     5  MIRNA_Domain
     6  Family_Name
     7  Precursor_Pos
     8  Predicted_Motif
     9  Mature_Name
    10  Mature_Pos
    11  High_Confidence
    12  Robust_FANTOM5
    13  Conserved_ADmiRE
    14  AF_Quantile_gnomAD
    15  HMDD_KnownDisease_PMID
    16  HMDD_ValidatedTargets_Disease_PMID
    17  miRTarBase_NumberOfTargets
    18  miRTarBase_TargetGene_ValidationType
    19  miRTarBase_Reference_PMID
    20  TranscriptionFactor_PMID
    21  Phylop_100way
    22  Phastcons_100way
    23  gnomAD_Count
    24  gnomAD_MAF
=cut

#!/usr/bin/perl
use warnings;
use strict;
use Getopt::Long qw(GetOptions);
use Pod::Usage;
use File::Basename;
my $dirname = dirname(__FILE__);

$"="\t";
my $input;
my $output;
my $admire_path= $dirname."/";
my $chr = "1";
my $pos = "2";
my $help;

GetOptions ("input|i=s" => \$input,    # string
            "output|o:s"   => \$output,      # string
            "admire_path|p:s"  => \$admire_path, # string
            "chr|c:i" => \$chr,    # numeric
            "pos|c:i" => \$pos,    # numeric
            'help|h' => \$help)  # flag
or die("Usage: perl annotate_admire.pl [--input FILE] [--output FILE] [--admire_path=PATH] [--chr=NUMBER] [--pos=NUMBER]\n");

if (defined $input) {
    } else {
    	print "Option input requires an argument
	Usage: perl annotate_admire.pl [--input FILE] [--output FILE] [--admire_path=PATH] [--chr=NUMBER] [--pos=NUMBER]\n";
	exit 1
}
if (defined $output) {
	} else {
    	$output=$input.".admire.tab";
}

##### READ ADMIRE INTO HASH	
my $input_db= $admire_path."ADmiRE.tab";
my %mirbase;
open FD, "<$input_db" or die "No Database";
foreach my $line_db (<FD>){
	$line_db =~ s/[\r\n]//g;
	my @entry_db = split (/\t/,$line_db);
	my $hash_key1=$entry_db[0]."_".$entry_db[1];
	my $hash_key2=$entry_db[3];
	my @hash_value= @entry_db[0..$#entry_db];	
	if ($entry_db[0] ne "Chromosome" ){push (@{$mirbase{$hash_key1}{$hash_key2}}, @hash_value);}
	}
close FD;

## READ VARIANT FILE AND ANNOTATE 
open FP, "<$input" or die "No Variant File";
open FO, ">$output" or die "No Output File";

my @empty;
push @empty, "NA" foreach(1..21);
$chr -= 1;
$pos -= 1;
ALLMUT: while (my $line_maf = <FP>){
	$line_maf =~ s/\r+\n$//g;
	#print $line_maf."\n";
	my @entry_maf = split ("\t",$line_maf);
	chomp @entry_maf;
	if ($line_maf =~ /^\#/ || $line_maf =~ /^CHROM/ || $line_maf =~ /^Hugo_Symbol/|| $line_maf =~ /^chr/) { print FO "@entry_maf\tMIRNA\tMIRNA_Domain\tFamily_Name\tPrecursor_Pos\tPredicted_Motif\tMature_Name\tMature_Pos\tHigh_Confidence\tRobust_FANTOM5\tConserved_ADmiRE\tAF_Quantile_gnomAD\tHMDD_KnownDisease_PMID\tHMDD_ValidatedTargets_Disease_PMID\tmiRTarBase_NumberOfTargets\tmiRTarBase_TargetGene_ValidationType\tmiRTarBase_Reference_PMID\tTranscriptionFactor_PMID\tPhylop_100way\tPhastcons_100way\tgnomAD_Count\tgnomAD_MAF\n";}
	elsif ($line_maf !~ /^\#/ && $line_maf !~ /^CHROM/ && $line_maf !~ /^Hugo_Symbol/) {
		my $db_key=$entry_maf[$chr]."_".$entry_maf[$pos];
		if ( keys %{$mirbase{$db_key}}){}
		else {print FO "@entry_maf\t@empty\n";next ALLMUT;}
		foreach my $db_key2 ( keys %{$mirbase{$db_key}}) {
			print FO "@entry_maf\t@{$mirbase{$db_key}{$db_key2}}[3..23]\n";
		   	}
		next ALLMUT;
		}
	}