--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tophat_stats_pe.xml	Wed Feb 06 09:56:58 2013 -0500
@@ -0,0 +1,38 @@
+<tool id="tophatstatsPE" name="Tophat Stats PE" version="1.0">
+  <description>Calculate mapping statistics from Tophat BAM files.</description>
+  <command interpreter="perl">tophatstatsPE.pl $hits $fastq > $output</command>
+  <inputs>
+    <param name="hits" type="data" format="bam" label="BAM file produced by Tophat"/>
+    <param name="fastq" type="data" format="fastq" label="Fastq file used to produce the BAM file" />
+  </inputs>
+  <outputs>
+    <data format="txt" name="output" />
+  </outputs>
+  <tests>
+  </tests>
+  <help>
+**Tophat Stats PE**
+
+This tool generates mapping statics from BAM files produced by
+Tophat. For paired-end experiments only one of the read files (R1
+or R2) needs to be provided.
+
+**Example output:**
+
+::
+
+  Input files: /galaxy/database/files/001/dataset_1682.dat         /galaxy/database/files/001/dataset_1680.dat
+  73538 total read pairs in fastq file
+  14429 (19.62%) read pairs with only one read in the pair mapped (14262 with unique alignments)
+  36461 (49.58%) read pairs mapped with correct orientation and insert size (36366 with unique alignments)
+  12169 (16.55%) read pairs mapped with correct orientation but wrong insert size (12063 with unique alignments)
+  0.458333333333333 (0.00%) read pairs mapped with wrong orientation but correct insert size (0 with unique alignments)
+  10478.5416666667 (14.25%) read pairs with no mapping
+
+
+**Credit**
+
+John Garbe,  University of Minnesota
+
+  </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tophatstatsPE.pl	Wed Feb 06 09:56:58 2013 -0500
@@ -0,0 +1,125 @@
+#!/usr/bin/perl -w
+
+############################################
+# tophatstatsPE
+# John Garbe
+# May 29, 2012
+#
+# Calculate statistics about the data going into and out of tophat:
+# -Count the number of raw reads, the number of aligned reads, the number 
+# of properly paired reads, etc
+#
+###########################################
+
+die "USAGE: tophatstats.pl accepted_hits.bam fastqfile.fastq\n" unless ($#ARGV == 1);
+
+$bamfile = $ARGV[0];
+$fastqfile = $ARGV[1];
+die "cannot open $fastqfile" unless (-e $fastqfile);
+die "cannot open $bamfile" unless (-e $bamfile);
+
+my $junk;
+$divide = 4; # four lines per read in a fastq file
+$insertsum = 0;
+$insertcount = 0;
+# count total number of raw reads
+if (1) {
+    print "Input files: $bamfile\t $fastqfile\n";
+    $results = `wc -l $fastqfile`;
+    ($results, $junk) = split ' ', $results;
+    $total = $results / $divide;
+    print "$total total read pairs in fastq file\n";
+}
+
+# read in bam file as a pipe from samtools
+open IFILE, "samtools view $bamfile |" or die "cannot open $bamfile\n";
+
+# initialize array counting multiple alignments
+for $i (0..200) {
+    $count[$i] = 0;
+    for $j (0..40) {
+	$unique[$i][$j] = 0;
+    }
+}
+
+$insertsum = 0;
+$insertcount = 0;
+# read through bam file, counting alignments
+while ($line = <IFILE>) {
+    @line = split /\t/, $line, 3;
+    $count[$line[1]]++;
+
+    # pull out number of alignments for this read
+    @line = split /\t/, $line, 12;
+    ($junk, $int) = split /NH:i:/, $line[11];
+    ($int, $junk) = split /\W/, $int;
+    if ($int == 1) { # count unique alignments
+	$unique[$line[1]][1]++;
+    } elsif ($int > 1) { # count non-unique alignments
+	$unique[$line[1]][2]+= 1 / $int;
+    }
+    if ($line[1] == 99 || $line[1] == 83) { # if proper insert size use for insert size average
+	@line = split /\t/, $line, 10;
+	$insertsum += $line[8];
+	$insertcount++;
+    }
+}
+
+# singleton
+$singleton_unique = 0;
+$singleton_multiple = 0;
+for $i (73, 133, 89, 121, 165, 181, 101, 117, 153, 185, 69, 137) {
+    $singleton_unique += $unique[$i][1];
+    $singleton_multiple += int($unique[$i][2]);
+}
+$singleton = $singleton_unique + $singleton_multiple;
+$singleton_percent = $singleton / $total * 100;
+printf "$singleton (%.2f%%) read pairs with only one read in the pair mapped ($singleton_unique with unique alignments)\n", $singleton_percent;
+
+# correct correct
+$correctcorrect_unique = 0;
+$correctcorrect_multiple = 0;
+for $i (99, 83) {
+    $correctcorrect_unique += $unique[$i][1];
+    $correctcorrect_multiple += int($unique[$i][2]);
+}
+$correctcorrect = $correctcorrect_unique + $correctcorrect_multiple;
+$correctcorrect_percent = $correctcorrect / $total * 100;
+printf "$correctcorrect (%.2f%%) read pairs mapped with correct orientation and insert size ($correctcorrect_unique with unique alignments)\n", $correctcorrect_percent;
+
+# correct wrong insert size
+$correctwrong_unique = 0;
+$correctwrong_multiple = 0;
+for $i (81, 97, 65, 113) {
+    $correctwrong_unique += $unique[$i][1];
+    $correctwrong_multiple += int($unique[$i][2]);
+}
+$correctwrong = $correctwrong_unique + $correctwrong_multiple;
+$correctwrong_percent = $correctwrong / $total * 100;
+printf "$correctwrong (%.2f%%) read pairs mapped with correct orientation but wrong insert size ($correctwrong_unique with unique alignments)\n", $correctwrong_percent;
+
+# correct wrong orientation
+$correctswitched_unique = 0;
+$correctswitched_multiple = 0;
+for $i (67, 115) {
+    $correctswitched_unique += $unique[$i][1];
+    $correctswitched_multiple += $unique[$i][2];
+}
+$correctswitched = $correctswitched_unique + $correctswitched_multiple;
+$correctswitched_percent = $correctswitched / $total * 100;
+printf "$correctswitched (%.2f%%) read pairs mapped with wrong orientation but correct insert size ($correctswitched_unique with unique alignments)\n", $correctswitched_percent;
+
+# no mapping
+$nomapping = $total - ($correctcorrect + $correctswitched + $correctwrong + $singleton);
+$nomapping_percent = $nomapping / $total * 100;
+printf "$nomapping (%.2f%%) read pairs with no mapping\n", $nomapping_percent;
+
+# insert size
+$insertavg = 0;
+$insertavg = $insertsum / $insertcount unless ($insertcount == 0);
+#printf "%.2fbp average inner distance between read pairs (of read pairs with correct insert size)\n", $insertavg; # Not ready for primetime yet - needs verification
+
+exit;
+
+############################################################
+