#
# Make your own RP sequence file
#
# This script will create a RP sequence file using the user's choices of
# Taxonomy Groups and RPG cutoffs.
#
# The perl module "LWP::Simple" is required
#
#!/usr/bin/perl

use LWP::Simple;
if(@ARGV != 2) {
	print "Usage: perl getMyRPSeq.pl mypick.txt output.seq\n";
	exit 1; 
}

# configuration file of tab-delimited txt file with three columns:
# TaxonGroup      TaxonId RPCutoff
# Note: for each row in the file, only the third column should be changed. 
# 	The possible values are 15, 35, 55, 75
my $mypick = $ARGV[0];

# path to the output sequence file
my $output = $ARGV[1];

my $url = 'http://pir.georgetown.edu/rps/data/rp_seq_tax_group/current/';
open(OUT, ">", $output) or die "Can't open $!\n";
open(PICK, $mypick) or die "Can't open $!\n";
while($line=<PICK>) {
	chomp($line);
	if(!($line =~ /^TaxonGroup/ || $line =~ /^#/ || $line =~ /^$/)) {
		($taxGroup, $taxId, $cutoff) = (split(/\t/, $line))[0, 1, 2];
		my $content = get $url."/".$cutoff."/".$taxId.".seq";
		die "Couldn't get $url" unless defined $content;
		print OUT $content;
	}
}
close(PICK);

close(OUT);