#!/usr/bin/env perl

use strict ;

use warnings ;

die "usage: a.pl bcrtcr.fa cgene.list species_name(Homo_sapiens or others)\n" if ( @ARGV == 0 ) ;

sub system_call

{

print STDERR "SYSTEM CALL: ".join(" ",@_)."\n";

system(@_) == 0

or die "system @_ failed: $?";

#print STDERR " finished\n";

}

my $species = $ARGV[2] ;

# Download

system_call( "wget -np -nd -r -A fasta -P tmp_download http://www.imgt.org//download/V-QUEST/IMGT_V-QUEST_reference_directory/".$species."/" ) ;

system_call( "cat tmp_download/*.fasta > tmp_download/vquest.fa") ;

# Reformat

#>J00256|IGHJ1*01|Homo sapiens|F|J-REGION|723..774|52 nt|1| | | | |52+0=52| | |

#

open FP1, "tmp_download/vquest.fa" ;

open FPout, ">IMGT+C.fa" ;

while ( <FP1> )

{

if ( !/^>/ )

{

$_ =~ tr/acgtn/ACGTN/ ;

print FPout $_ ;

next ;

}

print FPout ">".(split /\|/ )[1]."\n" ;

}

close FP1 ;

close FPout ;

# Append C gene from bcrtcr.fa

system_call( "grep -A 1 --no-group-separator -f ".$ARGV[1]." ".$ARGV[0]." >> IMGT+C.fa" ) ;

# remove the temporary download directory

rmdir "tmp_download"