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bin/geoCancerPrognosticDatasetsRetriever  view on Meta::CPAN

	}
}
############################ SUBROUTINE 11 #######################################################
#This subroutine uses regular expression analysis to detect prognostic signature patterns. 
#The regexes are based on over 50 parsed signatures used for different cancer types.
sub prognostic_signature_finder {

	my $soft_file             = $_[0];
	my %hash_signature        = ();
	my $soft_line             = "";
	my $regex_tail            = '(:|=)\s*(alive.*|no\sdeath|dea(d|th.*)|deceased|NED|DOD|DOC|0\s|1\s|no|yes|.*patient|died.*|alive|surviv(al|ed)|living|long|short|Y|N|NED|DOD|AWD|Exitus)';
	my $regex_keyword_type_A  = '(.*stat?us.*|.*(dea(d|th)|.*alive).*|.*\srecur\s.*|.*Die.*)' . $regex_tail;
	my $regex_keyword_type_B  = '(dss.?event\s?\(.+\)|dfs.*\w+|drfs.*|e\.dmfs.*|e\.rfs.*|e?\.?os.*)' . $regex_tail;
	my $regex_keyword_type_C  = '((Overall)?\s?survival.*|(overall)?.?event.*|outcome.*|prognosis.*|comort.*|evolution.*)' . $regex_tail;
	my $regex_keyword_type_Ca = '(Overall)?\s?survival\s.*(:|=)\s*(\d*)';
	my $outcome_1             = "Prognostic Signature filter: <Prognostic signature found>\n";
	my $outcome_2             = "Prognostic Signature filter: <No data found>\n";
	my $i                     = 0;
	
	#open SOFT file and read its contents
	open (KEY, "$run_dir/$soft_file") or die "Cannot open $soft_file: $!";