--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test/small_rna_map.bash	Mon Jul 24 06:28:45 2017 -0400
@@ -0,0 +1,43 @@
+#! /bin/bash
+# Execution command : bash small_rna_map.bash <sam file>
+samtools view -h -o input.sam ../test-data/input.bam
+samfile="input.sam"
+cut -f2,3,4,5,6 ../test-data/output.tab > test-data.dat
+grep -e "^@SQ" $samfile > header.tab
+cat $samfile | perl -ne 'print unless /^@/ or ( (split /\t/)[1] != 0 and (split /\t/)[1] != 16 )' > output1.tab
+
+cat << EOF > pyscript.py
+lendic = {}
+for line in open("header.tab"):
+  fields = line[:-1].split()
+  lendic[fields[1][3:]] = fields[2][3:]
+readdic = {}
+for line in (open("output1.tab")):
+  fields = line[:-1].split()
+  key = "-".join([fields[2],fields[3],"F" if fields[1]=="0" else "R"])
+  try:
+    readdic[key] += 1
+  except KeyError:
+    readdic[key] = 1
+Out = open("output.tab", "w")
+Out.write("Chromosome\tChrom_length\tCoordinate\tNbr_reads\tPolarity\n")
+for key in sorted(readdic):
+  fields = key.split("-")
+  Chromosome, Coordinate, Polarity = fields[0], fields[1], fields[2]
+  Chrom_length = lendic[Chromosome]
+  Nbr_reads = str(readdic[key])
+  Out.write("\t".join([Chromosome, Chrom_length, Coordinate, Nbr_reads, Polarity]) )
+  Out.write("\n")
+Out.close
+EOF
+
+python ./pyscript.py
+rm output1.tab header.tab pyscript.py
+sort -k 1,1 -k 3,3n -k 5,5  output.tab -o output.tab
+if ! diff -q output.tab test-data.dat &>/dev/null; then
+  >&2 echo "different"
+else
+  >&2 echo "Test passed"
+fi
+
+rm output.tab input.sam test-data.dat