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#!/usr/bin/perl
##############################################################################
# randomSplit
# randomly split a genbank file
#
# usage: randomSplit dbfile size
#
# dbfile: genbank file containing the genes
# size: size of the test set
# output: two files are created with names ending in .train
# and .test, being a training set and test set, respectively.
#
# This script is used by the braker.pl pipeline.
# Please be extremely careful when changing this script because the braker.pl
# pipeline may fail upon custom modification of this script.
# In case of doubt, contact katharina.hoff@uni-greifswald.de
#
# Mario Stanke, 24.06.2002
#############################################################################
srand 4;
if ($#ARGV != 1) {
print "$0: randomly split a genbank file in two subsets of given sizes\n";
print "usage: randomSplit dbfile size\n";
exit;
}
$dbfilename = $ARGV[0];
$size = $ARGV[1];
open (STDIN, $dbfilename);
@list = <STDIN>;
@namelines = grep /^LOCUS +/, @list;
if ($size > @namelines) {
print "size $size is greater than the number of genes in file\n",
"$dbfilename. Aborting.\n\n";
exit;
}
my %unique = ();
foreach (@namelines) {
/LOCUS +([^ ]+) */;
#print "$1\n";
push @names, "$1";
if(not(defined($unique{$1}))){$unique{$1} = 1;}else{
die( "ERROR in randomSplit.pl line 47: LOCUS names in genbank file are not unique!\n");
}
}
%testnames=();
while ($size--) {
$rand = rand (@names);
$testnames{$names[$rand]}=1;
splice @names, $rand, 1; # delete array element
}
open (TRAINFILE, ">${dbfilename}.train");
open (TESTFILE, ">${dbfilename}.test");
open (STDIN, $dbfilename);
#print "random test set:\n";
$/="\n//\n";
while(<STDIN>) {
$gendaten=$_;
m/^LOCUS +(\S+) .*/;
$genname=$1;
if (exists($testnames{$genname})) {
#print "$genname\n";
print TESTFILE "$gendaten";
} else {
print TRAINFILE "$gendaten";
}
}
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