diff gfapts/gfap_r1.0_known_var_finder.pl @ 1:028f435b6cfb draft default tip

Uploaded

--- a/gfapts/gfap_r1.0_known_var_finder.pl	Fri Jun 29 10:20:55 2012 -0400
+++ b/gfapts/gfap_r1.0_known_var_finder.pl	Fri Aug 03 05:50:41 2012 -0400
@@ -1,12 +1,91 @@
 #!/usr/bin/perl
 
 use strict;
-use lib 'inc/perlmod';
-use ngsutil qw[ :DEFAULT &varscan ];
+#use lib 'inc/perlmod';
+#use ngsutil qw[ :DEFAULT &varscan ];
 use warnings FATAL => qw[ numeric uninitialized ];
 use File::Basename;
 use Getopt::Long;
 
+#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+#	TEMP include ngsutil.pm
+sub explode_varcall{
+		my $N=0;
+		$_=shift @_ foreach my($POS, $REF, $ALT);
+		$_=$POS foreach my($START, $END);
+		my(@length, @range, @idx, @VAR, @POS);
+		@{$_}=() foreach (\@length, \@range, \@idx, \@VAR, \@POS);
+		push @length, length($_) foreach ($REF, $ALT);
+		@range=sort{ $a<=>$b } @length;
+		if($range[0]==1){
+			if($range[1]!=1){
+				foreach ($REF, $ALT){
+						$_=substr($_, 1);
+						$_=~s/^$/-/;
+					}
+				if($length[0]!=1){
+						$END+=$length[0]-1;
+						$START++;
+					}
+			}
+			push @POS, $START, $END;
+			push @VAR, $REF, $ALT;
+		}else{
+			my @N=();
+			undef $_ foreach my ($i, $VAR);
+			$_-=2 foreach (@length, @range);
+			$_++ foreach ($START, $END);
+			$_=substr($_, 1) foreach ($REF, $ALT);
+			my $indel='-' x ($range[1]-$range[0]);
+			$VAR.=($_>$range[0])?
+				('-'):((substr($REF, $_, 1) ne substr($ALT, $_, 1))?
+					0:1) for 0 .. $range[1];
+			$N++ while $VAR =~ /0/g;
+			if($length[0]<$length[1]){
+				@VAR=($VAR);
+				@N=($N);
+				$N=0;
+				undef($VAR);
+				$VAR.=($_>$range[0])?
+					('-'):((substr($REF, $length[0]-$_, 1) ne substr($ALT, $length[1]-$_, 1))?
+						0:1) for reverse 0 .. $range[1];
+				$N++ while $VAR =~ /0/g;
+				if($N>=$N[0]){ $N=shift(@N); $VAR=shift(@VAR); }
+				else{ $REF=$indel . $REF; }
+			}else{ $ALT.=$indel; }
+			foreach (qw[ 0 \- ]){
+					push @idx, [ $-[0], $+[0]-$-[0] ] while ($VAR =~ /$_+/g);
+				}
+			@{$_}=() foreach (\@VAR, \@POS);
+			foreach my $k (@idx){
+					push @VAR, substr($_, ${$k}[0], ${$k}[1]) || '-' foreach ($REF, $ALT);
+					push @POS, ${$k}[0], sum(@{$k})-1;
+				}
+			$_+=$START foreach @POS;
+			$_=~s/\-+/\-/ foreach @VAR;
+			for($i=0; $i<$#POS; $i+=2){ $POS[$i+1]=$POS[$i] if $VAR[$i] eq '-'; }
+		}
+		return(\@POS, \@VAR);
+	}
+
+sub varscan{
+		$_=shift @_ foreach my($kname, $fpath, $href);
+		my($k, @buffer);
+		open IN, "<$fpath" or die $!;
+		while(<IN>){
+				next if /^#/;
+				chomp;
+				@buffer=split /\s+/, $_;
+				next if !exists $$href{($k=join(':', @buffer[0..2]))};
+				next if $$href{$k}->{ref} !~ $buffer[3];
+				next if $$href{$k}->{alt} !~ $buffer[4];
+				splice(@buffer, 0, 5);
+				$$href{$k}->{$kname}=join(':', @buffer);
+			}
+		close IN;
+	}
+#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
 my($varfile, $buildver, $outdir, $dir_1000g, $dir_dbsnp, $dir_cosmic, $release_1000g, $release_dbsnp, $release_cosmic, $outfile, $k, @buffer, @varlist, %opts, %varlist);
 
 GetOptions(\%opts, "varfile=s", "buildver=s", "outdir=s", "dir_1000g=s", "dir_dbsnp=s", "dir_cosmic=s", "release_1000g=s", "release_dbsnp=s", "release_cosmic=s", "outfile=s");