Added extractor_loader.py to load DNA sequences from RAW files and put them...

Added extractor_loader.py to load DNA sequences from RAW files and put them through the Desciption Extractor

mutalyzer/extractor_loader.py

+#!/usr/bin/env python
+
+import sys
+
+import json
+
+import describe
+
+class MyEncoder(json.JSONEncoder):
+    def default(self, o):
+        return o.__dict__
+
+def main():
+    if len(sys.argv) < 3:
+        print "usage: " + sys.argv[0] + " reference sample"
+        exit()
+    #if
+
+    f = open(sys.argv[1], "r")
+    ref = f.read()
+    f.close()
+    f = open(sys.argv[2], "r")
+    alt = f.read()
+    f.close()
+
+    extracted_allele = describe.describe(ref, alt)
+
+    print describe.extractor.VERSION
+    print "HGVS: " + describe.allele_description(extracted_allele)
+    print "JSON: " + json.dumps({"reference_sequence": ref, "sample_sequence": alt, "allele_description": extracted_allele}, cls=MyEncoder)
+
+#main
+
+if __name__ == "__main__":
+    main()

mutalyzer/test.py

+#!/usr/bin/env python
+
+import json
+
+import describe
+
+class MyEncoder(json.JSONEncoder):
+    def default(self, o):
+        return o.__dict__
+
+def main():
+    ref = "ACGTCGATTCGCTAGCTTCGGGGGATAGATAGAGATATAGAGATATTTTT"
+    alt = "ACGTCGGTTCGCTAGCTTCGGGGGATAGATAGATATATAGAGATATTTTT"
+
+    extracted_allele = describe.describe(ref, alt)
+
+    print extracted_allele
+    print describe.allele_description(extracted_allele)
+    print json.dumps({"reference_sequence": ref, "sample_sequence": alt,
+        "allele_description": extracted_allele}, cls=MyEncoder)
+#main
+
+if __name__ == "__main__":
+    main()