Chris@1: #!/usr/bin/perl
Chris@1: 
Chris@1: # quick, very dirty little script so that we can put all the
Chris@1: # information for building a residue book set (except the original
Chris@1: # partitioning) in one spec file.
Chris@1: 
Chris@1: #eg:
Chris@1: 
Chris@1: # >res0_128_128 interleaved
Chris@1: # haux 44c0_s/resaux_0.vqd res0_96_128aux 0,4,2 9
Chris@1: # :1 res0_128_128_1.vqd, 4, nonseq cull, 0 +- 1
Chris@1: # :2 res0_128_128_2.vqd, 4, nonseq, 0 +- 1(.7) 2
Chris@1: # :3 res0_128_128_3.vqd, 4, nonseq, 0 +- 1(.7) 3 5
Chris@1: # :4 res0_128_128_4.vqd, 2, nonseq, 0 +- 1(.7) 3 5 8 11
Chris@1: # :5 res0_128_128_5.vqd, 1, nonseq, 0 +- 1 3 5 8 11 14 17 20 24 28 31 35 39 
Chris@1: 
Chris@1: 
Chris@1: die "Could not open $ARGV[0]: $!" unless open (F,$ARGV[0]);
Chris@1: 
Chris@1: $goflag=0;
Chris@1: while($line=<F>){
Chris@1: 
Chris@1:     print "#### $line";
Chris@1:     if($line=~m/^GO/){
Chris@1: 	$goflag=1;
Chris@1: 	next;
Chris@1:     }
Chris@1: 
Chris@1:     if($goflag==0){
Chris@1: 	if($line=~m/\S+/ && !($line=~m/^\#/) ){
Chris@1: 	    my $command=$line;
Chris@1: 	    print ">>> $command";
Chris@1: 	    die "Couldn't shell command.\n\tcommand:$command\n" 
Chris@1: 		if syst($command);
Chris@1: 	}
Chris@1: 	next;
Chris@1:     }
Chris@1: 
Chris@1:     # >res0_128_128
Chris@1:     if($line=~m/^>(\S+)\s+(\S*)/){
Chris@1: 	# set the output name
Chris@1: 	$globalname=$1;
Chris@1: 	$interleave=$2;
Chris@1: 	next;
Chris@1:     }
Chris@1: 
Chris@1:     # haux 44c0_s/resaux_0.vqd res0_96_128aux 0,4,2 9
Chris@1:     if($line=~m/^h(.*)/){
Chris@1: 	# build a huffman book (no mapping) 
Chris@1: 	my($name,$datafile,$bookname,$interval,$range)=split(' ',$1);
Chris@1:  
Chris@1: 	# check the desired subdir to see if the data file exists
Chris@1: 	if(-e $datafile){
Chris@1: 	    my $command="cp $datafile $bookname.tmp";
Chris@1: 	    print ">>> $command\n";
Chris@1: 	    die "Couldn't access partition data file.\n\tcommand:$command\n" 
Chris@1: 		if syst($command);
Chris@1: 
Chris@1: 	    my $command="huffbuild $bookname.tmp $interval";
Chris@1: 	    print ">>> $command\n";
Chris@1: 	    die "Couldn't build huffbook.\n\tcommand:$command\n" 
Chris@1: 		if syst($command);
Chris@1: 
Chris@1: 	    my $command="rm $bookname.tmp";
Chris@1: 	    print ">>> $command\n";
Chris@1: 	    die "Couldn't remove temporary file.\n\tcommand:$command\n" 
Chris@1: 		if syst($command);
Chris@1: 	}else{
Chris@1: 	    my $command="huffbuild $bookname.tmp 0-$range";
Chris@1: 	    print ">>> $command\n";
Chris@1: 	    die "Couldn't build huffbook.\n\tcommand:$command\n" 
Chris@1: 		if syst($command);
Chris@1: 
Chris@1: 	}
Chris@1: 	next;
Chris@1:     }
Chris@1: 
Chris@1:     # :1 res0_128_128_1.vqd, 4, nonseq, 0 +- 1
Chris@1:     if($line=~m/^:(.*)/){
Chris@1: 	my($namedata,$dim,$seqp,$vals)=split(',',$1);
Chris@1: 	my($name,$datafile)=split(' ',$namedata);
Chris@1: 	# build value list
Chris@1: 	my$plusminus="+";
Chris@1: 	my$list;
Chris@1: 	my$thlist;
Chris@1: 	my$count=0;
Chris@1: 	foreach my$val (split(' ',$vals)){
Chris@1: 	    if($val=~/\-?\+?\d+/){
Chris@1: 		my$th;
Chris@1: 
Chris@1: 		# got an explicit threshhint?
Chris@1: 		if($val=~/([0-9\.]+)\(([^\)]+)/){
Chris@1: 		    $val=$1;
Chris@1: 		    $th=$2;
Chris@1: 		}
Chris@1: 
Chris@1: 		if($plusminus=~/-/){
Chris@1: 		    $list.="-$val ";
Chris@1: 		    if(defined($th)){
Chris@1: 			$thlist.="," if(defined($thlist));
Chris@1: 			$thlist.="-$th";
Chris@1: 		    }
Chris@1: 		    $count++;
Chris@1: 		}
Chris@1: 		if($plusminus=~/\+/){
Chris@1: 		    $list.="$val ";
Chris@1: 		    if(defined($th)){
Chris@1: 			$thlist.="," if(defined($thlist));
Chris@1: 			$thlist.="$th";
Chris@1: 		    }
Chris@1: 		    $count++;
Chris@1: 		}
Chris@1: 	    }else{
Chris@1: 		$plusminus=$val;
Chris@1: 	    }
Chris@1: 	}
Chris@1: 	die "Couldn't open temp file $globalname$name.vql: $!" unless
Chris@1: 	    open(G,">$globalname$name.vql");
Chris@1: 	print G "$count $dim 0 ";
Chris@1: 	if($seqp=~/non/){
Chris@1: 	    print G "0\n$list\n";
Chris@1: 	}else{	
Chris@1: 	    print G "1\n$list\n";
Chris@1: 	}
Chris@1: 	close(G);
Chris@1: 
Chris@1: 	my $command="latticebuild $globalname$name.vql > $globalname$name.vqh";
Chris@1: 	print ">>> $command\n";
Chris@1: 	die "Couldn't build latticebook.\n\tcommand:$command\n" 
Chris@1: 	    if syst($command);
Chris@1: 
Chris@1: 	if(-e $datafile){
Chris@1: 	
Chris@1: 	    if($interleave=~/non/){
Chris@1: 		$restune="res1tune";
Chris@1: 	    }else{
Chris@1: 		$restune="res0tune";
Chris@1: 	    }
Chris@1: 	    
Chris@1: 	    if($seqp=~/cull/){
Chris@1: 		my $command="$restune $globalname$name.vqh $datafile 1 > temp$$.vqh";
Chris@1: 		print ">>> $command\n";
Chris@1: 		die "Couldn't tune latticebook.\n\tcommand:$command\n" 
Chris@1: 		    if syst($command);
Chris@1: 	    }else{
Chris@1: 		my $command="$restune $globalname$name.vqh $datafile > temp$$.vqh";
Chris@1: 		print ">>> $command\n";
Chris@1: 		die "Couldn't tune latticebook.\n\tcommand:$command\n" 
Chris@1: 		    if syst($command);
Chris@1: 	    }
Chris@1: 
Chris@1: 	    my $command="mv temp$$.vqh $globalname$name.vqh";
Chris@1: 	    print ">>> $command\n";
Chris@1: 	    die "Couldn't rename latticebook.\n\tcommand:$command\n" 
Chris@1: 		if syst($command);
Chris@1: 
Chris@1: 	}else{
Chris@1: 	    print "No matching training file; leaving this codebook untrained.\n";
Chris@1: 	}
Chris@1: 
Chris@1: 	my $command="rm $globalname$name.vql";
Chris@1: 	print ">>> $command\n";
Chris@1: 	die "Couldn't remove temp files.\n\tcommand:$command\n" 
Chris@1: 	    if syst($command);
Chris@1: 
Chris@1: 	next;
Chris@1:     }
Chris@1: }
Chris@1: 
Chris@1: $command="rm -f temp$$.vqd";
Chris@1: print ">>> $command\n";
Chris@1: die "Couldn't remove temp files.\n\tcommand:$command\n" 
Chris@1:     if syst($command);
Chris@1: 
Chris@1: sub syst{
Chris@1:     system(@_)/256;
Chris@1: }