Add error checking when shelling out (#15)

stjude · May 27, 2020 · d469af3 · d469af3
1 parent 57485b9
commit d469af3
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Showing 5 changed files with 99 additions and 11 deletions.
diff --git a/src/bin/Cicero.pl b/src/bin/Cicero.pl
@@ -166,9 +166,18 @@
 
 my $sam_d = Bio::DB::Sam->new( -bam => $input_bam, -fasta => $ref_genome);
 
-system("touch $out_dir/unfiltered.fusion.txt"); 
-system("touch $out_dir/unfiltered.internal.txt"); 
-
+my $ret = system("touch $out_dir/unfiltered.fusion.txt"); 
+if ($ret){
+	my $err = $!;
+	print STDERR "Error sorting blat output: $err\n"; 
+	exit $err;
+}
+$ret = system("touch $out_dir/unfiltered.internal.txt"); 
+if ($ret){
+	my $err = $!;
+	print STDERR "Error sorting blat output: $err\n"; 
+	exit $err;
+}
 # the softclip file is sorted, so no need to re-sort it
 open my $SCLIP, "<$sclip_file" or croak "can't open $sclip_file:$OS_ERROR";
 while( my $line = <$SCLIP> ) {

diff --git a/src/bin/annotate.pl b/src/bin/annotate.pl
@@ -156,10 +156,24 @@
 my $unfiltered_file = "$out_dir/unfiltered.fusion.txt";
 if($internal) { 
 	$unfiltered_file = "$out_dir/unfiltered.internal.txt";
-	`cat $out_dir/*/unfiltered.internal.txt > $unfiltered_file` unless(-s $unfiltered_file);
+	unless (-s $unfiltered_file){
+		`cat $out_dir/*/unfiltered.internal.txt > $unfiltered_file`;
+		if ($?){
+			my $err = $!;
+			print STDERR "Error combining internal events: $err\n"; 
+			exit $err;
+		}		
+	}
 }
 else{
-	`cat $out_dir/*/unfiltered.fusion.txt > $unfiltered_file` unless(-s $unfiltered_file);
+	unless (-s $unfiltered_file){
+		`cat $out_dir/*/unfiltered.fusion.txt > $unfiltered_file`;
+		if ($?){
+			my $err = $!;
+			print STDERR "Error combining fusion events: $err\n"; 
+			exit $err;
+		}
+	}
 }
 print "Unfiltered fusions file: $unfiltered_file\n"; 
 
@@ -561,8 +575,18 @@ sub is_bad_fusion{
 
 print STDERR "out file is: $out_file\nnumber of SVs: ", scalar @raw_SVs, "\n" if($debug);
 `mkdir  -p $out_dir/tmp_anno`;
+if ($?){
+	my $err = $!;
+	print STDERR "Error creating annotation directory: $err\n"; 
+	exit $err;
+}
 my $annotation_dir = tempdir(DIR => "$out_dir/tmp_anno");
 `mkdir -p $annotation_dir`;
+if ($?){
+	my $err = $!;
+	print STDERR "Error creating temp directory for annotation: $err\n"; 
+	exit $err;
+}
 print STDERR "Annotation Dir: $annotation_dir\n" if($debug); 
 
 print STDERR "Reading cover files\n"; 
@@ -1222,6 +1246,11 @@ sub quantification {
 		$arg .= " $fa_file2 " if (-f $fa_file2 && -s $fa_file2);
 		if ($arg ne ""){
 			`cat $arg >> $fa_file`; 
+      if ($?){
+			  my $err = $!;
+			  print STDERR "Error creating fasta file: $err\n"; 
+			  exit $err;
+		  } 
 		}
 		#`cat $fa_file1 >> $fa_file` if(-f $fa_file1 && -s $fa_file1);
 		#`cat $fa_file2 >> $fa_file` if(-f $fa_file2 && -s $fa_file2);
@@ -1283,8 +1312,22 @@ sub quantification {
 		my ($psl_file1, $psl_file2) = ("$anno_dir/bp1.psl", "$anno_dir/bp2.psl",);
 
 		unlink $psl_file1 if(-f $psl_file1); unlink $psl_file2 if(-f $psl_file2);
-		`blat -noHead -maxIntron=5 $tmp_ctg_file $fa_file1 $psl_file1` if(-s $fa_file1);
-		`blat -noHead -maxIntron=5 $tmp_ctg_file $fa_file2 $psl_file2` if(-s $fa_file2);
+		if (-s $fa_file1){
+			`blat -noHead -maxIntron=5 $tmp_ctg_file $fa_file1 $psl_file1`;
+			if ($?){
+				my $err = $!;
+				print STDERR "Error running blat: $err\n"; 
+				exit $err;
+			}
+		}
+		if (-s $fa_file2){
+			`blat -noHead -maxIntron=5 $tmp_ctg_file $fa_file2 $psl_file2`;
+			if ($?){
+				my $err = $!;
+				print STDERR "Error running blat: $err\n"; 
+				exit $err;
+			}
+		}
 		my ($readsA, $areaA, $readsB, $areaB) = (0,1,0,1);
 		my $shift_bases = 5;
 		if($chrA eq $bp1->{tname} && abs($bp1->{tpos} - $tposA)<50 &&

diff --git a/src/bin/get_geneInfo.pl b/src/bin/get_geneInfo.pl
@@ -90,6 +90,11 @@
 $sample=$bam_file[0] unless (defined $sample);
 
 `mkdir -p $out_dir`;
+if ($?){
+	my $err = $!;
+	print STDERR "Error creating output directory: $err\n"; 
+	exit $err;
+}
 
 my %blacklist = ();
 if($blacklist_file && -s $blacklist_file){

diff --git a/src/bin/prepareCiceroInput.pl b/src/bin/prepareCiceroInput.pl
@@ -82,7 +82,14 @@
 close $GI;
 
 my $SC_file = "$out_dir/$out_prefix.SC.txt";
+
 `ls $out_dir/$out_prefix*.cover | xargs cat > $SC_file`;
+if ($?){
+	my $err = $!;
+	print STDERR "Error combining cover files: $err\n"; 
+	exit $err;
+}
+
 print STDERR $SC_file, "\n";
 open my $SCI, "$SC_file";
 

diff --git a/src/perllib/CiceroExtTools.pm b/src/perllib/CiceroExtTools.pm
@@ -62,7 +62,12 @@ sub run {
 		print STDERR "$file is of size 0";
 		return;
 	}
-	system(join(" ", ($self->{PRG}, $file, $self->{OPTIONS})));
+	my $ret = system(join(" ", ($self->{PRG}, $file, $self->{OPTIONS})));
+	if ($ret){
+		my $err = $!;
+		print STDERR "Error running assembler: $err\n"; 
+		exit $err;
+	}
 	my( $r_count, $r_reads ) = _count_reads("$file.cap.ace");
 	return ("$file.cap.contigs", $r_count, $r_reads, "$file.cap.singlets");
 }
@@ -152,6 +157,11 @@ sub run {
 	print STDERR "\ntest=$test\t", join(" ", ($self->{PRG}, $self->{BIT2_DIR}, $param{-QUERY}, $unsorted_psl, $options)), "\n" if($debug);
 	# Sort the output PSL file from BLAT.
 	`sort -k 11,11nr -k 10,10d -k 14,14d -k 1,1nr $unsorted_psl -o $psl_file`;
+	if ($?){
+		my $err = $!;
+		print STDERR "Error sorting blat output: $err\n"; 
+		exit $err;
+	}
 
 	# Instantiate a parser and load the results into an array to pass to subroutines for checks.
 	# A "result" is everything for a given query
@@ -952,6 +962,11 @@ sub overhang_remapping {
 
 	return unless(-s $unsorted_psl);
 	`sort -k 10,10d -k 14,14d -k 1,1nr $unsorted_psl -o $psl_file`;
+	if ($?){
+		my $err = $!;
+		print STDERR "Error sorting blat output: $err\n"; 
+		exit $err;
+	}
 
 	#print "sc site is $scSite\n";
 	my ($max_length, $max_percent, $total_matches) = (0, 0);
@@ -1640,17 +1655,26 @@ sub run {
 	croak "Missing QUERY parameter for $self->{PRG}" if(!$param{-QUERY});
 	my $output = $param{-OUTPUT} || $param{-QUERY} . ".psl";
 	my $opt = $self->{OPTIONS} . " -maxIntron=1 ";
-	system( join(" ", ($self->{PRG}, $param{-TARGET}, $param{-QUERY}, $output, $opt)));
+	my $ret = system( join(" ", ($self->{PRG}, $param{-TARGET}, $param{-QUERY}, $output, $opt)));
+	if ($ret){
+		my $err = $!;
+		print STDERR "Error running aligner: $err\n"; 
+		exit $err;
+	}
 	my $rtn = _find_best_hit($output);
 	if( scalar(keys(%{$rtn})) > 0) {
 		return $output if($param{-FILE});
 		return $rtn;
 	}
 	$opt = $self->{OPTIONS} . " -fastMap ";
-	system( join(" ", ($self->{PRG}, $param{-TARGET}, $param{-QUERY}, $output, $opt)));
+	my $ret = system( join(" ", ($self->{PRG}, $param{-TARGET}, $param{-QUERY}, $output, $opt)));
+	if ($ret){
+		my $err = $!;
+		print STDERR "Error running aligner: $err\n"; 
+		exit $err;
+	}
 	return $output if($param{-FILE});
 	return _find_best_hit($output);
-
 }
 
 sub _find_best_hit {