debugging in get_hmm

MGEScan · Feb 8, 2016 · b33bc17 · b33bc17
1 parent d11bf61
commit b33bc17
Showing 1 changed file with 17 additions and 2 deletions.
diff --git a/mgescan/nonltr/hmm/get_phmm.pl b/mgescan/nonltr/hmm/get_phmm.pl
@@ -1,6 +1,13 @@
 #!/usr/bin/perl
 use strict; 
 use Getopt::Long;
+use Cwd 'abs_path';
+use File::Basename;
+use lib dirname (dirname abs_path $0) . '/lib';
+use Prompt qw(prompt_yn);
+
+my $debug;
+$debug = $ENV{'MGESCAN_DEBUG'};
 
 my $seq; 
 my $phmm_file;
@@ -48,7 +55,12 @@
 	($fh, $tmpfile) = tempfile( UNLINK => 1, SUFFIX => '.tbl');
 	#system("hmmconvert ".$phmm_file." > ".$phmm_file."c");
 	#system("hmmsearch  --noali --domtblout ".$phmm_dir."tbl ".$phmm_file."c ".$pep_file." > /dev/null");
-	system("hmmsearch  --noali --domtblout ".$tmpfile." ".$phmm_file."3 ".$pep_file." > /dev/null");
+	my $hmm_command = ("hmmsearch  --noali --domtblout ".$tmpfile." ".$phmm_file."3 ".$pep_file." > /dev/null");
+	print $hmm_command if ($debug);
+	if ($debug && not prompt_yn("Continue?")) {
+		exit;
+	}
+	system($hmm_command);
 	local $/ = undef;
 	my $hmm_result = <$fh>;
 	close $fh;
@@ -68,7 +80,10 @@
 	}
 }else{
 	$command = "hmm2search ".$phmm_file." ".$pep_file;
-	#print $command;
+	print $command if ($debug);
+	if ($debug && not prompt_yn("Continue?")) {
+		exit;
+	}
 	$hmm_result = `$command`;
 
 	@hmm_results = split(/\n/, $hmm_result);