Script to postprocess pmatch, needs doc...

misc-scripts/protein_match/process_pmach.pl

+#use strict;
+use Getopt::Long;
+
+my ($ens,$sp,$refseq);
+
+&GetOptions(
+            
+            'ens:s'=>\$ens,
+            'sp:s'=>\$sp,
+            'refseq:s'=>\$refseq
+            );
+
+&runpmatch();
+&postprocesspmatch($sp);
+&postprocesspmatch($refseq);
+&finalprocess($sp);
+&finalprocess($refseq);
+
+sub runpmatch {
+    print STDERR "Running pmatch\n";
+ 
+#Run pmatch and store the data in files which will be kept for debugging
+    my $pmatch1 = "/nfs/griffin2/rd/bin.ALPHA/pmatch $sp $ens > ens_sp_rawpmatch";
+    my $pmatch2 = "/nfs/griffin2/rd/bin.ALPHA/pmatch $refseq $ens > ens_refseq_rawpmatch";
+    
+    system($pmatch1);# == 0 or die "$0\Error running '$pmatch1' : $!";
+    system($pmatch2);# == 0 or die "$0\Error running '$pmatch2' : $!";
+}
+
+
+    
+sub postprocesspmatch {
+    my ($db) = @_;
+    my %hash1;
+    
+       #open (OUT, ">../data/$db.processed");
+#Post process the raw data from pmatch
+    if ($db eq $sp) {
+	print STDERR "Postprocessing pmatch for SP mapping\n";
+	open (OUT, ">ens_sp.processed");
+	open (PROC, "ens_sp_rawpmatch");
+    }
+    
+    else {
+	print STDERR "Postprocessing pmatch for REFSEQ mapping\n"; 
+	open (OUT, ">ens_refseq.processed");
+	open (PROC, "ens_refseq_rawpmatch") || die "Can't open file ens_refseq_rawpmatch\n";
+    }
+    
+    while (<PROC>) {
+	## 20      Q9UN99  36      55      8.1     ENSP00000051351 63      82      7.8
+	my ($len,$id,$start,$end,$perc,$query,$qst,$qend,$qperc) = split;
+	#print STDERR "$id:$query";
+	my $uniq = "$id:$query";
+	
+	$hash1{$uniq} += $qperc;
+    }
+
+
+
+    foreach my $key ( keys %hash1 ) {
+	($a,$b) = split(/:/,$key);
+	print OUT "$a\t$b\t$hash1{$key}\n";
+    }
+   close (OUT);                               
+}
+
+sub finalprocess {
+    my ($db) = @_;
+    
+    if ($db eq $sp) {
+	print STDERR "Getting final mapping for SP mapping\n";
+	open (PROC, "ens_sp.processed");
+	open (OUT, ">ens_sp.final");
+    }
+
+    else {
+	print STDERR "Getting final mapping for REFSEQ mapping\n";
+	open (PROC, "ens_refseq.processed") || die "Can' open file ens_refseq.processed\n";
+	open (OUT, ">refseq.final");
+    }
+
+    my %hash2;
+    while (<PROC>) {
+	my ($ens,$known,$perc) = split;
+	#if ($perc > 100) {
+	 #   print "$ens\t$known\t$perc\n";
+	#}
+	if( !defined $hash2{$known} ) {
+	    $hash2{$known} = [];
+	}
+	
+	$p= NamePerc->new;
+	$p->name($ens);
+	$p->perc($perc);
+	
+	push(@{$hash2{$known}},$p);
+    }
+
+
+    foreach my $know ( keys %hash2 ) {
+	@array = @{$hash2{$know}};
+	@array = sort { $b->perc <=> $a->perc } @array;
+	
+	$top = shift @array;
+	print  OUT "$know\t",$top->name,"\t",$top->perc,"\tPRIMARY\n";
+	
+	foreach $ens ( @array ) {
+	    if( $ens->perc > $top->perc ) {
+		die "Not good....";
+	    }
+	}
+	
+	if (scalar(@array) >= 20) {
+	    foreach my $repeat (@array) {
+		print OUT "$know\t",$repeat->name,"\t",$repeat->perc,"\tREPEAT\n";
+	    }
+	}
+	
+	if (scalar(@array) < 20) {
+	    foreach my $duplicate (@array) {
+		if( $duplicate->perc+1 >= $top->perc ) {
+		    print OUT "$know\t",$duplicate->name,"\t",$duplicate->perc,"\tDUPLICATE\n";
+		}
+		else {
+		    print OUT "$know\t",$duplicate->name,"\t",$duplicate->perc,"\tPSEUDO\n";
+		}
+	    } 
+	}              
+    } 
+    close (OUT);
+}
+
+
+package NamePerc;
+
+
+sub new {
+    my $class= shift;
+    my $self = {};
+    bless $self,$class;
+    return $self;
+}
+
+
+=head2 name
+
+ Title   : name
+ Usage   : $obj->name($newval)
+ Function:
+ Returns : value of name
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub name{
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'name'} = $value;
+    }
+    return $obj->{'name'};
+
+}
+
+=head2 perc
+
+ Title   : perc
+ Usage   : $obj->perc($newval)
+ Function:
+ Returns : value of perc
+ Args    : newvalue (optional)
+
+
+=cut
+
+sub perc{
+   my $obj = shift;
+   if( @_ ) {
+      my $value = shift;
+      $obj->{'perc'} = $value;
+    }
+    return $obj->{'perc'};
+
+}                    
+
+