update_HGNC_symbols.pl

#!/usr/local/bin/perl
use strict;
use warnings;

use HTTP::Tiny;
use JSON;
use Encode;
use Data::Dumper;

use Getopt::Long;


#parameters
my $man = "USAGE : search_hgnc.pl
\n--file <gene symbol file> (mandatory)
\n--symbolColumn <number of column that contains gene symbol (default =1 for first)>
\n--noHGNC_ID <this args will prevent a supplementary hgnc_id containing column to be add >
\n\n-v|--version < return version number and exit > ";

my $help;
my $version = "search_hgnc version 1.0.0";
my $file = "";
my @file_List = "";
my $file_line = "";
my $symbolCol = 1;
my $noHGNC;



my $http = HTTP::Tiny->new();

my $response = "";
my $server = 'https://rest.genenames.org';
my $request_type = '/search/';
my $query = '';
my $result = "";



GetOptions(     "file=s"                         => \$file,
			    "symbolColumn:s"   => \$symbolCol,
				"noHGNC_ID"		=> \$noHGNC,		 
				"help"		=> \$help,
			    "version|v"   => \$version);


if(defined $help){
	print("$man\n");
	exit(0);
}

if($file eq ""){
	die("$man\n");
}



$symbolCol = $symbolCol -1 ;

my $output = $file."_HGNC_Checked.txt";

my $notEmptyField = 0;
my $header = 0;
my $emptyField = 0;
my $notFound = 0;
my $changedField = 0;
my $unchangedField = 0;

#file treatment
if($file ne ""){

	
	open(INPUT , "<$file") or die("Cannot open file ".$file) ;
	
	open(OUTPUT , '>' , $output) or die $!;

	print  STDERR "Processing input file ... \n" ;
	while( <INPUT> ){
		$file_line = $_;
		#############################################
		##############   skip header
	
		
		chomp $file_line;
		@file_List = split( /\t/, $file_line );
				
		if ($file_line=~/^#/){
			unless(defined $noHGNC){push(@file_List,"hgnc_id")};
			print OUTPUT join("\t",@file_List)."\n";
			$header++;
			print  STDERR "Skip header ... \n" ;
			next;
		}
		if ($file_line=~/^gene/){
			unless(defined $noHGNC){push(@file_List,"hgnc_id")};
			print OUTPUT join("\t",@file_List)."\n";
			$header++;
			print  STDERR "Skip header ... \n" ;
			next;
		}

		############### skip empty field ###########
		if (! defined $file_List[$symbolCol] || $file_List[$symbolCol] eq ""){
			unless(defined $noHGNC){push(@file_List,"")};
			print OUTPUT join("\t",@file_List)."\n";
			$emptyField++;
			next;
		}
		
		$notEmptyField++;

		$query=$file_List[$symbolCol];
		print "\n".$query;

		$response = $http->get($server.$request_type.$query, {headers => { 'Accept' => 'application/json' }	});

		die "Failed!\n" if $response->{status} ne '200';
		my $json_bytes = encode('UTF-8', $response->{content});
		my $result = decode_json($json_bytes);
		
		if ($result->{response}->{numFound} < 1){
			unless(defined $noHGNC){push(@file_List,"")};
			print OUTPUT join("\t",@file_List)."\n";
			$notFound ++ ;
			print "\t-->\tnot Found";
		}else{
			
			print "\t-->\t".$result->{response}->{docs}[0]{hgnc_id};

			if ($file_List[$symbolCol] eq $result->{response}->{docs}[0]{symbol}){
				$unchangedField++;
			}else{
				$changedField++;
				$file_List[$symbolCol]=$result->{response}->{docs}[0]{symbol};
				print "\t-->\t".$file_List[$symbolCol];
			}
			unless(defined $noHGNC){	
				push(@file_List,$result->{response}->{docs}[0]{hgnc_id});
				$file_List[-1] =~ s/HGNC://;
			}
			print OUTPUT join("\t",@file_List)."\n";
		}

	}
		
	close(INPUT);
}
		
close(OUTPUT);

print STDERR "Done..............\n";
print STDERR "Header lines: ".$header."\n";
print STDERR "Empty symbol field: ".$emptyField."\n";
print STDERR "Not Empty fields: ".$notEmptyField."\n";
print STDERR "Symbol not found: ".$notFound."\n";
print STDERR "Symbol has changed: ".$changedField."\n";
print STDERR "Symbol is the same: ".$unchangedField."\n";





#my $statement = q{There are %d genes that contain the phrase } .
#q{"MAP kinase interacting" } .
#q{within the approved name which have the locus type} .
#q{"gene with protein product"};

#printf $statement, $result->{response}->{numFound};
#printf $result->{response}->{numFound};
#printf $result->{response}->{docs}[0]{hgnc_id};
#print Dumper($result);
exit 0;