Fixing a bug which caused prep to filter out all the drugs

ding-lab · Dec 5, 2017 · 843d071 · 843d071
1 parent ddebbe2
commit 843d071
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Showing 6 changed files with 16 additions and 11 deletions.
diff --git a/README.md b/README.md
@@ -10,7 +10,7 @@ Usage
 
          Stable:     v0.6.0 
 
-           Beta:     up to v1.8.1
+           Beta:     up to v1.8.2
         
          Author:     Beifang Niu, John Wallis, Adam D Scott, Sohini Sengupta, & Amila Weerasinghe
 

diff --git a/bin/hotspot3d b/bin/hotspot3d
@@ -2,13 +2,13 @@
 #----------------------------------
 # $Authors: Beifang Niu & Adam D Scott
 # $Date: 2013-08-08 13:22:08 -0500 (Thu Aug  8 13:22:08 CDT 2013) $
-# $Revision: 1.8.1 $
+# $Revision: 1.8.2 $
 # $URL: $
 #----------------------------------
 use strict;
 use warnings;
 
-our $VERSION = 'V1.8.1';
+our $VERSION = 'V1.8.2';
 
 use Carp;
 use FileHandle;

diff --git a/dist.ini b/dist.ini
@@ -1,6 +1,6 @@
 name    = HotSpot3D
 author  = Beifang Niu, John Wallis, Adam D Scott, Sohini Sengupta, Amila Weerasinghe, & Matthew H Bailey from McDonnell Genome Institute of Washington University at St. Louis
-version = 1.8.1
+version = 1.8.2
 license = Perl_5
 copyright_holder = McDonnell Genome Institute at Washington University
 copyright_year   = 2017

diff --git a/lib/TGI/Mutpro/Preprocess/Calpro.pm b/lib/TGI/Mutpro/Preprocess/Calpro.pm
@@ -300,7 +300,7 @@ sub writeProximityFile {
 			# Get AminoAcid object for residue in chain '$uniprotChain', 
 			# at position $position
 			$uniprotAminoAcidRef = $$peptideRef{$uniprotChain}->getAminoAcidObject( $residuePosition );
-			next if ( $$uniprotAminoAcidRef->isAA() == 0 );
+			next if ( $$uniprotAminoAcidRef->isHOH() == 1 );
 			$uniprotAaName = $$uniprotAminoAcidRef->name();
 			# 	Updated	170510 : use a hash with chain and regions for retrieving the offset
 			$uniprotChainOffset = getOffset( $allOffsets, $uniprotChain, $residuePosition );
@@ -339,7 +339,7 @@ sub writeProximityFile {
 				foreach $position ( sort {$a<=>$b} @tmp_array_positions ) {
 					$otherChainOffset = getOffset( $allOffsets, $chain, $position );
 					$aaObjRef = $$peptideRef{$chain}->getAminoAcidObject($position);
-					next if ( $$aaObjRef->isAA() == 0 );
+					next if ( $$aaObjRef->isHOH() == 1 );
 					if ( (defined $otherChainOffset) and ($otherChainOffset eq "N/A") ) { 
 						$correctedPosition = $position;
 					} else { 
@@ -526,7 +526,7 @@ sub checkOffsets {
 		next if ( $uniprotB !~ /^\w+$/ || $offsetA !~ /^-?\d+$/ || $offsetB !~ /^-?\d+$/ || $positionA !~ /^-?\d+$/ || $positionB !~ /^-?\d+$/ );
 		$aminoAcidA = TGI::Mutpro::Preprocess::PdbStructure::convertAA( $aminoAcidA );
 		$aminoAcidB = TGI::Mutpro::Preprocess::PdbStructure::convertAA( $aminoAcidB );
-		next if ( !defined $aminoAcidA || !defined $aminoAcidB );
+		next if ( !defined $aminoAcidA & !defined $aminoAcidB );
 		#next unless ( TGI::Mutpro::Preprocess::AminoAcid::checkAA( $aminoAcidA ) and TGI::Mutpro::Preprocess::AminoAcid::checkAA( $aminoAcidB )
 		if ( defined $pdbUniprotPosition{$pdbId}{$uniprotA}{$positionA+$offsetA} && $pdbUniprotPosition{$pdbId}{$uniprotA}{$positionA+$offsetA} ne $aminoAcidA ) {
 			print $coorfh "Inconsistent amino acids for $uniprotA position $positionA+$offsetA in $pdbId: '$pdbUniprotPosition{$pdbId}{$uniprotA}{$positionA+$offsetA}' and $aminoAcidA \n";

diff --git a/lib/TGI/Mutpro/Preprocess/PdbStructure.pm b/lib/TGI/Mutpro/Preprocess/PdbStructure.pm
@@ -533,6 +533,7 @@ sub convertAA {
     # Convert single amino acid code to triplet
     # or triplet to single amino acid code
     my $residue = $_[0];
+    my $convertedAA = undef;
     $residue = uc $residue;
     my %oneToThree =  (
 		       A => 'ALA',
@@ -563,8 +564,8 @@ sub convertAA {
     }elsif ( defined $threeToOne{$residue} ) {
 	return $threeToOne{$residue};
     }elsif ( length( $residue ) <= 3 ) {
-        length( $residue ) == 1 ? return "Z" : return $residue;
-    } else { carp "Unrecognized format for amino acid '$residue'"; }
+        length( $residue ) == 1 ? return "Z" : return $convertedAA;
+    } else { return $convertedAA; carp "Unrecognized format for amino acid '$residue'"; }
 }
 
 sub printStructure {

diff --git a/lib/TGI/Mutpro/Preprocess/Uppro.pm b/lib/TGI/Mutpro/Preprocess/Uppro.pm
@@ -22,6 +22,7 @@ use List::MoreUtils qw( uniq );
 
 use TGI::Mutpro::Preprocess::Uniprot;
 use TGI::Mutpro::Preprocess::HugoGeneMethods;
+use TGI::Files::File;
 use TGI::Files::MAF;
 use TGI::Files::List;
 
@@ -168,8 +169,8 @@ sub process {
         $fh->print( "\t$alias_list\n" );
     }
     $fh->close();
-	my $cmd_list_submit_file_fh;
-    unless( open ( $cmd_list_submit_file_fh, ">", $this->{'cmd_list_submit_file'} ) ) { die "HotSpot3D Uppro Error: Could not open cmd file (".$this->{'cmd_list_submit_file'}.")"; }
+	my $cmd_list_submit_file_fh = new FileHandle; #TGI::Files::File->new( $this->{'cmd_list_submit_file'} ) ;
+        unless( $cmd_list_submit_file_fh -> open ( $this->{'cmd_list_submit_file'}, "w" ) )  { die "HotSpot3D Uppro Error: Could not open cmd file (".$this->{'cmd_list_submit_file'}.")"; }
 	print STDOUT "Creating ".$this->{'cmd_list_submit_file'}."\n";
 	my $command = "";
 	if ( $this->{'parallel'} eq $BSUB ) {
@@ -215,12 +216,15 @@ sub makeBSUBCalproCommand {
 sub makeSerialCalproCommand {
 	my ( $this , $inpro_dir , $cmd_list_submit_file_fh , $uniprotid_toupdate ) = @_;
     my $log_dir = "$this->{'output_dir'}\/Logs\/";
+	my $serialCommand = "echo Serially Running Calpro Commands";
 	map {
 		system("touch $inpro_dir/$_.ProximityFile.csv");
 		my $command = $this->makeCalproCommand( $_ );
 		print STDOUT $command."\n"; 
 		$cmd_list_submit_file_fh->print( $command."\n" );
+		$serialCommand .= ";".$command;
 	} keys %{$uniprotid_toupdate};
+	return $serialCommand;
 }
 
 sub makeLocalCalproCommand {