--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/FeaturesParser.py	Tue Jun 24 12:16:43 2014 -0400
@@ -0,0 +1,64 @@
+#!/usr/bin/python
+# python parser module to analyse Features in sRbowtie alignments (guided by a GFF3 file)
+# version 0.9
+# Usage FeaturesParser.py  <1:index source> <2:extraction directive> <3:output> <4:GFF3 guide file> <5:6:7 filePath:FileExt:FileLabel> <.. ad  lib>
+
+import sys
+from smRtools import *
+from collections import *
+
+IndexSource = sys.argv[1]
+ExtractionDirective = sys.argv[2]
+if ExtractionDirective == "--do_not_extract_index":
+  genomeRefFormat = "fastaSource"
+elif  ExtractionDirective == "--extract_index":
+  genomeRefFormat = "bowtieIndex"
+Output = sys.argv[3]
+GFF3_file = sys.argv[4]
+Triplets = [sys.argv[5:][i:i+3] for i in xrange(0, len(sys.argv[5:]), 3)]
+MasterListOfGenomes = {}
+FeatureDict = defaultdict(dict)
+
+for [filePath, FileExt, FileLabel] in Triplets:
+  MasterListOfGenomes[FileLabel] = HandleSmRNAwindows (filePath, FileExt, IndexSource, genomeRefFormat) 
+  FeatureDict[FileLabel] = MasterListOfGenomes[FileLabel].CountFeatures(GFF3=GFF3_file)
+
+# add some code to pick up the GFF3 features in their order of appearence.
+F = open(GFF3_file, "r")
+featureList = []
+for line in F:
+  if line[0] == "#": continue
+  feature = line.split()[2]
+  if feature not in featureList:
+    featureList.append(feature)
+F.close()
+
+header = ["#Feature"]
+for [filePath, FileExt, FileLabel] in Triplets:
+  header.append(FileLabel)
+
+F = open (sys.argv[3], "w")
+print >> F, "\t".join(header)
+for feature in  featureList:
+  line=[feature]
+  for sample in header[1:]:
+    count = str (FeatureDict[sample][feature])
+# uncomment to get percentage in addition to counts
+#    percent = float(FeatureDict[sample][feature]) / MasterListOfGenomes[sample].alignedReads
+#    value = "%s | %0.2f" % (count, percent)
+#    line.append(value)
+    line.append(count)
+  print >> F,  "\t".join(line )
+line = ["Unfeatured"]
+for sample in header[1:]:
+  matched = 0
+  for feature in FeatureDict[sample]:
+    matched += FeatureDict[sample][feature]
+  unmatched = MasterListOfGenomes[sample].alignedReads - matched
+# uncomment to get percentage in addition to counts
+#  percent = float (unmatched) / (matched + unmatched)
+#  value = "%s | %0.2f" % (unmatched, percent)
+#  line.append(value)
+  line.append("%s" % unmatched)
+print >> F,  "\t".join(line)
+F.close()