--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MirParser.py	Sun Jun 22 18:31:14 2014 -0400
@@ -0,0 +1,81 @@
+#!/usr/bin/python
+# python parser module for pre-mir and mature miRNAs, guided by mirbase.org GFF3
+# version 0.0.9 (1-6-2014)
+# Usage MirParser.py  <1:index source> <2:extraction directive> <3:output pre-mir> <4: output mature miRs> <5:mirbase GFF3>
+#                     <6:pathToLatticeDataframe or "dummy_dataframe_path"> <7:Rcode or "dummy_plotCode"> <8:latticePDF or "dummy_latticePDF">
+#                     <9:10:11 filePath:FileExt:FileLabel> <.. ad  lib>
+
+import sys, subprocess
+from smRtools import *
+
+IndexSource = sys.argv[1]
+ExtractionDirective = sys.argv[2]
+if ExtractionDirective == "--do_not_extract_index":
+  genomeRefFormat = "fastaSource"
+elif  ExtractionDirective == "--extract_index":
+  genomeRefFormat = "bowtieIndex"
+OutputPre_mirs = sys.argv[3]
+OutputMature_Mirs = sys.argv[4]
+GFF3_file = sys.argv[5]
+lattice = sys.argv[6]
+Rcode = sys.argv[7]
+latticePDF = sys.argv[8]
+Triplets = [sys.argv[9:][i:i+3] for i in xrange(0, len(sys.argv[9:]), 3)]
+MasterListOfGenomes = {}
+
+for [filePath, FileExt, FileLabel] in Triplets:
+  print FileLabel
+  MasterListOfGenomes[FileLabel] = HandleSmRNAwindows (alignmentFile=filePath, alignmentFileFormat=FileExt, genomeRefFile=IndexSource, genomeRefFormat=genomeRefFormat, biosample=FileLabel) 
+
+header = ["gene"]
+for [filePath, FileExt, FileLabel] in Triplets:
+  header.append(FileLabel)
+
+hit_table = ["\t".join(header)] # table header: gene, sample1, sample2, sample3, etc. separated by tabulation
+
+## read GFF3 to subinstantiate
+gff3 = open (GFF3_file, "r")
+lattice_dataframe = []
+for line in gff3:
+  if line[0] == "#": continue
+  gff_fields = line[:-1].split("\t")
+  chrom = gff_fields[0]
+  gff_name = gff_fields[-1].split("Name=")[-1].split(";")[0] # to isolate the GFF Name
+  item_upstream_coordinate = int(gff_fields[3])
+  item_downstream_coordinate = int(gff_fields[4])
+  if gff_fields[6] == "+":
+    item_polarity = "forward"
+  else:
+    item_polarity = "reverse"
+  item_line = [gff_name]
+  for sample in header[1:]:
+    count = MasterListOfGenomes[sample].instanceDict[chrom].readcount(upstream_coord=item_upstream_coordinate, downstream_coord=item_downstream_coordinate, polarity=item_polarity)
+    item_line.append(str(count))
+    ## subtreatement for lattice
+    if lattice != "dummy_dataframe_path":
+      if ("5p" not in gff_name) and  ("3p" not in gff_name):
+        lattice_dataframe.append(MasterListOfGenomes[sample].instanceDict[chrom].readcoverage(upstream_coord=item_upstream_coordinate, downstream_coord=item_downstream_coordinate, windowName=gff_name+"_"+sample) )
+    ## end of subtreatement for lattice
+  hit_table.append("\t".join(item_line) )
+gff3.close()
+
+Fpremirs = open (OutputPre_mirs, "w")
+print >> Fpremirs, hit_table[0]
+finalPreList = [ i for i in sorted(hit_table[1:]) if ("5p" not in i) and  ("3p" not in i)] 
+print >> Fpremirs, "\n".join(finalPreList )
+Fpremirs.close()
+
+Fmaturemires = open (OutputMature_Mirs, "w")
+print >> Fmaturemires, hit_table[0]
+finalMatureList = [ i for i in sorted(hit_table[1:]) if ("5p" in i) or ("3p" in i)]
+print >> Fmaturemires, "\n".join(finalMatureList )
+Fmaturemires.close()
+
+if lattice != "dummy_dataframe_path":
+  Flattice = open(lattice, "w")
+  print >> Flattice, "%s\t%s\t%s\t%s\t%s\t%s\t%s" % ("sample", "mir", "offset", "offsetNorm", "counts","countsNorm",  "polarity")
+  print >> Flattice, "\n".join(lattice_dataframe)
+  Flattice.close()
+  R_command="Rscript "+ Rcode
+  process = subprocess.Popen(R_command.split())
+  process.wait()