diff sRbowtieParser.py @ 0:3a510730e3fc draft

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sRbowtieParser.py	Mon Nov 03 10:27:20 2014 -0500
@@ -0,0 +1,45 @@
+#!/usr/bin/python
+# python parser module to analyse sRbowtie alignments
+# version 1.0.0 - argparse implementation
+# Usage sRbowtieParser.py  <1:index source> <2:extraction directive> <3:outputL> <4:polarity> <5:6:7 filePath:FileExt:FileLabel> <.. ad  lib>
+
+import sys, argparse
+from smRtools import *
+
+def Parser():
+  the_parser = argparse.ArgumentParser()
+  the_parser.add_argument('--IndexSource', action="store", type=str, help="Path to the index source")
+  the_parser.add_argument('--ExtractDirective', action="store", type=str, choices=["fastaSource", "bowtieIndex"], help="Extract info from fasta or bowtie index")
+  the_parser.add_argument('--output', action="store", type=str, help="path to the output")
+  the_parser.add_argument('--polarity', choices=["forward", "reverse", "both"], help="forward, reverse or both forward an reverse reads are counted")
+  the_parser.add_argument('--alignmentSource',nargs='+', help="paths to alignments files")
+  the_parser.add_argument('--alignmentFormat',nargs='+', help="Format of the bowtie alignment (tabular, sam or bam)")
+  the_parser.add_argument('--alignmentLabel',nargs='+', help="Label of the alignment")
+  args = the_parser.parse_args()
+  return args
+
+args = Parser()
+
+IndexSource = args.IndexSource
+genomeRefFormat = args.ExtractDirective
+Output = args.output
+Polarity = args.polarity
+MasterListOfGenomes = {}
+
+for filePath, FileExt, FileLabel in zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel):
+  MasterListOfGenomes[FileLabel] = HandleSmRNAwindows (filePath, FileExt, IndexSource, genomeRefFormat) 
+
+header = ["gene"]
+for filePath, FileExt, FileLabel in zip (args.alignmentSource, args.alignmentFormat, args.alignmentLabel):
+  header.append(FileLabel)
+
+F = open (args.output, "w")
+# print >>F, args
+print >> F, "\t".join(header)
+for item in sorted (MasterListOfGenomes[header[1]].instanceDict.keys() ):
+  line=[item]
+  for sample in header[1:]:
+    count = str (MasterListOfGenomes[sample].instanceDict[item].readcount(polarity=Polarity))
+    line.append(count)
+  print >> F,  "\t".join(line )
+F.close()