From 7bc8e6839e6825e559bf92504460e19454138d49 Mon Sep 17 00:00:00 2001
From: jkvis <jvis@liacs.nl>
Date: Mon, 28 Jul 2014 15:28:06 +0200
Subject: [PATCH] Added extractor_loader.py to load DNA sequences from RAW
files and put them through the Desciption Extractor
---
mutalyzer/extractor_loader.py | 35 +++++++++++++++++++++++++++++++++++
mutalyzer/test.py | 24 ++++++++++++++++++++++++
2 files changed, 59 insertions(+)
create mode 100644 mutalyzer/extractor_loader.py
create mode 100644 mutalyzer/test.py
diff --git a/mutalyzer/extractor_loader.py b/mutalyzer/extractor_loader.py
new file mode 100644
index 00000000..7401efd3
--- /dev/null
+++ b/mutalyzer/extractor_loader.py
@@ -0,0 +1,35 @@
+#!/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()
diff --git a/mutalyzer/test.py b/mutalyzer/test.py
new file mode 100644
index 00000000..d4939025
--- /dev/null
+++ b/mutalyzer/test.py
@@ -0,0 +1,24 @@
+#!/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()
--
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