debugging in perl

MGEScan · Feb 7, 2016 · 71829d7 · 71829d7
1 parent a1b4fbe
commit 71829d7
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Showing 3 changed files with 52 additions and 14 deletions.
diff --git a/mgescan/nonltr/lib/Prompt.pm b/mgescan/nonltr/lib/Prompt.pm
@@ -0,0 +1,24 @@
+package Prompt;
+use strict;
+use warnings;
+
+use Exporter qw(import);
+
+our @EXPORT_OK = qw(prompt_yn);
+
+# http://stackoverflow.com/a/18104317
+sub prompt {
+	my ($query) = @_; # take a prompt string as argument
+	local $| = 1; # activate autoflush to immediately show the prompt
+	print $query;
+	chomp(my $answer = <STDIN>);
+	return $answer;
+}
+
+sub prompt_yn {
+	my ($query) = @_;
+	my $answer = prompt("$query (Y/n): ");
+	return lc($answer) ne 'n';
+}
+
+1;
diff --git a/mgescan/nonltr/run_MGEScan.pl b/mgescan/nonltr/run_MGEScan.pl
@@ -4,9 +4,12 @@
 use Cwd 'abs_path';
 use File::Basename;
 use Sys::Hostname;
+use lib (dirname abs_path $0) . '/lib';
+use Prompt qw(prompt_yn);
 
 my $program_dir = dirname(abs_path($0))."/";
 
+
 ############################################
 # INPUT
 ############################################
@@ -99,7 +102,10 @@
 			my $plus_dna_file = $plus_dna_dir.$name;
 			my $command = $program_dir."run_hmm.pl --dna=".$plus_dna_file."  --out=".$plus_out_dir." --hmmerv=".$hmmerv;
 			printf $command."\n" if ($debug);
-			#system($command);
+			if ($debug and not prompt_yn("continue?")) {
+				exit;
+			}
+			system($command);
 		}
 	}
 }
@@ -112,7 +118,10 @@
 
 my $command = $program_dir."post_process.pl --dna=".$plus_dna_dir." --out=".$plus_out_dir." --rev=0";
 printf $command."\n" if ($debug);
-#system($command);
+if ($debug and not prompt_yn("continue?")) {
+	exit;
+}
+system($command);
 
 
 ############################################
@@ -136,8 +145,12 @@
 		if ($name !~ /^\./){  
 			my $minus_dna_file = $minus_dna_dir.$name;
 			my $command = $program_dir."run_hmm.pl --dna=".$minus_dna_file." --out=".$minus_out_dir." --hmmerv=".$hmmerv;
-			#system($command);
 			printf $command."\n" if ($debug);
+			if ($debug and not prompt_yn("continue?")) {
+				exit;
+			}
+			system($command);
+
 		}
 	}
 }
@@ -147,16 +160,22 @@
 system("rm -f ".$minus_out_dir."out1/qqqqq.*");
 
 my $command = $program_dir."post_process.pl --dna=".$minus_dna_dir." --out=".$minus_out_dir." --rev=1";
-printf $command."\n";
-#system($command);
+printf $command."\n" if ($debug);
+if ($debug and not prompt_yn("continue?")) {
+	exit;
+}
+system($command);
 
 ###########################################
 #validation for Q value
 ###########################################
 
 my $command = $program_dir."post_process2.pl --data_dir=".$main_data_dir." --hmmerv=".$hmmerv;
-#system($command);
 printf $command."\n" if ($debug);
+if ($debug and not prompt_yn("continue?")) {
+	exit;
+}
+system($command);
 
 system("rm -rf ".$minus_dna_dir);
 

diff --git a/mgescan/nonltr/run_hmm.pl b/mgescan/nonltr/run_hmm.pl
@@ -4,6 +4,7 @@
 use Cwd 'abs_path';
 use File::Basename;
 use File::Temp qw/ tempfile unlink0 /;
+user prompt;
 
 my $pdir = dirname(abs_path($0))."/";
 my $phmm_dir = $pdir."pHMM/";
@@ -68,16 +69,9 @@
 		close(OUT);
 	}
 
-	$command = $pdir."match_pos.pl -rt=".$domain_rt_pos_file." -ape=".$domain_ape_pos_file;
-	#system($command);
-	###########################################################
-	# run hmm
-	###########################################################
-	#print "Running HMM...\n";
-
 	$out_file = $out1_dir.$dna_name;
 	$command = $pdir."hmm/MGEScan -m ".$pdir."hmm/chr.hmm -s ".$dna_file." -r ".$domain_rt_pos_file." -a ".$domain_ape_pos_file." -o ".$out_file." -p ".$pdir." -d ".$out1_dir." -v ".$hmmerv;
-	#print $command."\n";
+	print $command."\n" if ($debug);
 	system($command); 
 }
 
@@ -249,3 +243,4 @@ sub get_sequence{  # file name, variable for seq, variable for head
 	close(GENOME);
 }
 
+