--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2.4/src/standalone_blat2.pl	Mon Jun 02 07:35:53 2014 -0400
@@ -0,0 +1,267 @@
+#!/usr/bin/perl -sw
+use Getopt::Long;
+sub usage(){
+    print "
+    Usage: <VCF> -g <genome.2bit> -seq|s <seq.fa> -f genome.fa 
+	-o out.vcf
+	-n contig.names
+        -dist   how wide of a window to look for bp [50]\n
+	-v	verbose option
+        Requires samtools,bedTools, and blat in your path\n;
+        ";
+    die;
+}
+#Initialize values
+my ($blat,$genome,$tei_bed,$vntr_bed,$out_vcf,$contig_names,$contig,$fasta,$uninformative_contigs,$dist,$verbose,$bedTools,$samtools);
+GetOptions ("genome|g=s" => \$genome,
+            "o|out:s" => \$out_vcf,
+            "names|n:s" => \$contig_names,
+            "seq|s=s" => \$contig,
+            "f|fasta:s" => \$fasta,
+	    "b|bad:s" => \$uninformative_contigs,
+            "dist:s" => \$dist,
+	    "v" => \$verbose
+	    );
+#$genome="/data2/bsi/reference/db/hg19.2bit""
+#$blat="/projects/bsi/bictools/apps/alignment/blat/34/blat" ;
+#TEI.bed=egrep "LINE|SINE|LTR" /data5/bsi/epibreast/m087494.couch/Reference_Data/Annotations/hg19.repeatMasker.bed >TEI.bed
+#VNTR_BED=egrep "Satellite|Simple_repeat" /data5/bsi/epibreast/m087494.couch/Reference_Data/Annotations/hg19.repeatMasker.bed > VNTR.bed
+
+
+$blat=`which blat`;
+if (!$blat) {die "Your do not have BLAT in your path\n\n"}
+$samtools=`which samtools`;
+if (!$samtools) {die "Your do not have samtools in your path\n\n"}
+$bedTools=`which sortBed`;
+if (!$bedTools) {die "Your do not have bedTools in your path\n\n"}
+
+
+if (!$dist) {$dist=50}
+if (!$out_vcf) {$out_vcf="out.vcf"}
+if (!$contig_names) {$contig_names="contig.names"}
+if (!$uninformative_contigs) {$uninformative_contigs="uninformative.contigs"}
+
+if ((!$genome)||(!$contig)||(!$fasta)){&usage;die;}
+
+
+open(VCF,"$ARGV[0]") or die "must specify VCF file\n\n";
+open(OUT_VCF,">",$out_vcf) or die "can't open the output VCF\n";
+open(CONTIG_LIST,">",$contig_names) or die "can't open the contig names\n";
+open(BAD_CONTIG_LIST,">",$uninformative_contigs) or die "can't open the contig names\n";
+#print "writing to CONTIG_LIST=$contig_names\n";
+while (<VCF>) {
+    if($_=~/^#/){
+        if ($.==1) {
+            print OUT_VCF $_;
+            print OUT_VCF "##INFO=<ID=STRAND,Number=1,Type=String,Description=\"Strand to which assembled contig aligned\">\n";
+            print OUT_VCF "##INFO=<ID=CONTIG,Number=1,Type=String,Description=\"Name of assembeled contig matching event\">\n";
+            print OUT_VCF "##INFO=<ID=MECHANISM,Number=1,Type=String,Description=\"Proposed mechanism of how the event arose\">\n";
+            print OUT_VCF "##INFO=<ID=INSLEN,Number=1,Type=Integer,Description=\"Length of insertion\">\n";
+            print OUT_VCF "##INFO=<ID=HOM_LEN,Number=1,Type=Integer,Description=\"Length of microhomology\">\n"; 
+            next;
+        }
+    else {
+        print OUT_VCF $_;
+        next;
+        }
+    };
+    chomp;
+
+    ##look for exact location of BP
+    @line=split("\t",$_);
+    my($left_chr,$start,$end);
+
+    #Get left position
+    $left_chr=$line[0];
+    $start=$line[1]-$dist;
+    $end=$line[1]+$dist;
+
+    #Get right position
+    my ($mate_pos,@mate,$mate_chr,$mate_start,$mate_end);
+    $mate_pos=$line[4];
+    $mate_pos=~s/[\[|\]|A-Z]//g;
+    #print "mate_pos=$mate_pos\n";
+    @mate=split(/:/,$mate_pos);
+    $mate_chr=$mate[0]; $mate_pos=$mate[1];
+    $mate_start=$mate_pos-$dist;$mate_end=$mate_pos+$dist;
+    #print "$left_chr:$start-$end\n$mate_chr:$mate_start-$mate_end\n";
+    
+    #Run through blat
+    my ($result1,$result2);
+    my $target1=join("",$left_chr,":",$start,"-",$end);
+    my $target2=join("",$mate_chr,":",$mate_start,"-",$mate_end);
+    #print "target1=$target1\ttarget2=$target2\n";die;
+    $result1=get_result($target1);
+    $result2=get_result($target2);
+   
+
+    my $NOV_INS="";
+    #If there is a NOV_INS, then there shouldn't be any output, so trick the results
+    if ($_=~/EVENT=NOV_INS/) {
+        $mate_start=$start;
+        $NOV_INS="true";
+        if (!$result1) {$result1=join("\t","0","0","0","0","0","0","0","0","+","UNKNOWN_NODE","0","0",$dist);}
+        if (!$result2) {$result2=join("\t","0","0","0","0","0","0","0","0","+","UNKNOWN_NODE","0","0",$dist);}
+   }
+    
+    #Skip over events that aren't supported
+    if ((!$result1)||(!$result2)){
+	my @tmp1=split("\t",$result1);
+	my @tmp2=split("\t",$result2);
+	if ($tmp1[9]) {print BAD_CONTIG_LIST "$tmp1[9]\n"}
+	if ($tmp2[9]) {print BAD_CONTIG_LIST "$tmp2[9]\n" }
+	next;
+    }
+    #Parse blat results   
+    my @result1=split("\t",$result1);
+    my @result2=split("\t",$result2);
+if($result2[9] ne $result1[9]){print "$result2[9] != $result1[9]\n";next}
+    #print "@result1\n@result2\n";die;
+    my $pos1=$start+($result1[12]-$result1[11]);
+    my $pos2=$mate_start+($result2[12]-$result2[11]);
+    #print "$_\n$pos1\t$pos2\n";
+    
+    ##############################################################
+    ### Build Classifier
+    
+    my ($QSTART1,$QEND1,$QSTART2,$QEND2,$len,$MECHANISM, $INSERTION, $DELETION, $bed_res1,$bed_res2);
+    $MECHANISM="UNKNOWN";
+    $len="UNKNOWN";
+    #Make sure the later event is second
+    if ($result1[11] <  $result2[11]){
+	$QSTART1=$result1[11];
+	$QEND1=$result1[12];
+	$QSTART2=$result2[11];
+	$QEND2=$result2[12];
+    }
+    else{
+	$QSTART1=$result2[11];
+	$QEND1=$result2[12];
+	$QSTART2=$result1[11];
+	$QEND2=$result1[12];
+    }
+    #Now calculate the difference between $QEND1 and QSTART2
+    if($verbose){print "QEND1=$QEND1\tQSTART2=$QSTART2\n";}
+    $len=$QEND1-$QSTART2;
+    #Check for TEI
+    if($_=~/MECHANISM=TEI/){$MECHANISM="TEI"}
+    elsif($_=~/MECHANISM=VNTR/){$MECHANISM="VNTR"}
+    else{
+        if ($len==0) {$MECHANISM="NHEJ"}
+	else{
+	    if ($len>0){$INSERTION="true"}
+		if ($len<0){$DELETION="true"}
+		    if ($INSERTION){
+		        if ($len>10) {$MECHANISM="FOSTES"}
+		        else{$MECHANISM="NHEJ"}
+		    }
+		elsif ($DELETION){
+		    if ($len>100) {$MECHANISM="NAHR"}
+		        elsif ($len > 2){$MECHANISM="altEJ"}
+		        else{$MECHANISM="NHEJ"}
+	        }
+	    }	
+	}
+
+    
+#if ($verbose){print "@result1";print "@result2";}
+
+    #print out VCF
+    #############################################################
+    # create temporary variable name
+    #############################################################
+    srand (time ^ $$ ^ unpack "%L*", `ps axww | gzip -f`);
+    my $random_name=join "", map { ("a".."z")[rand 26] } 1..8;
+    my $random_name2=join "", map { ("a".."z")[rand 26] } 1..8;
+   
+   #Get Ref Base
+   my ($ref_base,$alt_base,$tmp_mate_pos);
+   $ref_base=getBases($left_chr,$pos1,$fasta);
+   $alt_base=getBases($mate_chr,$pos2,$fasta);#print "ALT=$alt_base\n";
+   #Substitute the new mate position and base
+   $tmp_mate_pos=$line[4];
+   $tmp_mate_pos=~s/$mate_pos/$pos2/;
+   $tmp_mate_pos=~s/[A-Z]/$alt_base/;
+   #split apart the INFO field to adjust the ISIZE and MATEID
+   my $NEW_INFO="";
+   my @INFO=split(/;/,$line[7]);
+   for (my $i=0;$i<@INFO;$i++){
+        if ($INFO[$i] =~ /^ISIZE=/){
+            my @tmp=split(/=/,$INFO[$i]);
+            $NEW_INFO.="ISIZE=";
+            my $new_ISZIE=$pos2-$pos1;
+            $NEW_INFO.=$new_ISZIE
+            }
+        elsif($INFO[$i] =~ /^MATE_ID=/){
+            $NEW_INFO.=";MATE_ID=".$random_name2 . ";";
+        }
+        else{
+            $NEW_INFO.=$INFO[$i].";";
+        }
+   }
+   #ADD in strand and name
+   $NEW_INFO.="STRAND=".$result1[8];
+   $NEW_INFO.=";CONTIG=".$result1[9];
+   if($MECHANISM!~/TEI|VNTR/){$NEW_INFO.=";MECHANISM=".$MECHANISM;}
+    $NEW_INFO.=";HOM_LEN=".$len;
+   #don't pring contig nage if its a novel insertion
+   if(!$NOV_INS){print CONTIG_LIST "$result1[9]\n";}#else{print "I'm not printing $result1[9]\n";}
+    print OUT_VCF "$left_chr\t$pos1\t$random_name\t$ref_base\t$tmp_mate_pos\t1000\tPASS\t$NEW_INFO\t$line[8]\t$line[9]\n";
+    #Now go through and fill info in for mate
+    #Substitute the new mate position and base
+   $tmp_mate_pos=$line[4];
+   $tmp_mate_pos=~s/$mate_pos/$pos1/;
+   $tmp_mate_pos=~s/[A-Z]/$ref_base/;
+   $tmp_mate_pos=~s/$mate_chr/$left_chr/;
+    $NEW_INFO="";
+    @INFO=split(/;/,$line[7]);
+   for (my $i=0;$i<@INFO;$i++){
+    if ($INFO[$i] =~ /^ISIZE=/){
+            my @tmp=split(/=/,$INFO[$i]);
+            $NEW_INFO.="ISIZE=";
+            my $new_ISZIE=$pos2-$pos1;
+            $NEW_INFO.=$new_ISZIE
+            }
+        elsif($INFO[$i] =~ /^MATE_ID=/){
+            $NEW_INFO.=";MATE_ID=".$random_name.";";
+        }
+        else{
+            $NEW_INFO.=$INFO[$i].";";
+        }
+   }
+    #ADD in strand and name
+   $NEW_INFO.="STRAND=".$result2[8];
+   $NEW_INFO.=";CONTIG=".$result2[9];
+   if ($MECHANISM!~/TEI|VNTR/){$NEW_INFO.=";MECHANISM=".$MECHANISM;}
+    $NEW_INFO.=";HOM_LEN=".$len;
+
+   #don't pring contig nage if its a novel insertion
+   if(!$NOV_INS){print CONTIG_LIST "$result2[9]\n";} #else{print "I'm not printing $result1[9]\n";}
+    print OUT_VCF "$mate_chr\t$pos2\t$random_name2\t$alt_base\t$tmp_mate_pos\t1000\tPASS\t$NEW_INFO\t$line[8]\t$line[9]\n";
+	if ($verbose){print  "$mate_chr\t$pos2\t$random_name2\t$alt_base\t$tmp_mate_pos\t1000\tPASS\t$NEW_INFO\t$line[8]\t$line[9]\n";}
+}
+close VCF;
+close OUT_VCF;
+close CONTIG_LIST;
+close BAD_CONTIG_LIST;
+sub get_result{
+        my $target=($_[0]);
+if($verbose){print "target=$target\n"}#;die;
+        my $cmd="blat $genome:$target $contig /dev/stdout -t=dna -q=dna -noHead|egrep -v \"Searched|Loaded\" |head -1";
+
+if ($verbose){print "$cmd\n"}        #print "$cmd\n";die;
+        my $result=`$cmd`;
+        next if (!$cmd);
+        return ($result);
+}
+sub getBases{
+        my ($chr,$pos1,$fasta)=@_;
+        my @result=();
+        if ($pos1 <0){print "$pos1 is not a valid position (likely caused by circular MT chromosome)\n";$result[1]="NA";};
+        @result = `samtools faidx $fasta $chr:$pos1-$pos1`;
+        if(!$result[1]){$result[1]="NA"};
+        chomp($result[1]);
+        return uc($result[1]);
+}
+
+