From 141ad7f2087644eea728f8e773e90e739314e6d5 Mon Sep 17 00:00:00 2001
From: jkvis <jvis@liacs.nl>
Date: Wed, 6 Aug 2014 10:51:40 +0200
Subject: [PATCH] Removed debug information
---
mutalyzer/describe.py | 15 +++++++--------
mutalyzer/extractor_loader.py | 6 +++---
mutalyzer/test.py | 1 -
3 files changed, 10 insertions(+), 12 deletions(-)
diff --git a/mutalyzer/describe.py b/mutalyzer/describe.py
index 520322ba..246a5d1a 100644
--- a/mutalyzer/describe.py
+++ b/mutalyzer/describe.py
@@ -303,14 +303,13 @@ def describe_dna(s1, s2):
description = Allele()
in_transposition = 0
- variant_extract = extractor.extract(str(s1), len(s1), str(s2), len(s2), 0)
- for variant in variant_extract.variants:
- print (variant.type, variant.reference_start,
- variant.reference_end, variant.sample_start,
- variant.sample_end, variant.transposition_start,
- variant.transposition_end)
- print (variant.type & extractor.TRANSPOSITION_OPEN, variant.type &
- extractor.TRANSPOSITION_CLOSE)
+ for variant in extractor.extract(unicode(s1), len(s1), unicode(s2), len(s2), 0):
+ # print (variant.type, variant.reference_start,
+ # variant.reference_end, variant.sample_start,
+ # variant.sample_end, variant.transposition_start,
+ # variant.transposition_end)
+ # print (variant.type & extractor.TRANSPOSITION_OPEN, variant.type &
+ # extractor.TRANSPOSITION_CLOSE)
if variant.type & extractor.TRANSPOSITION_OPEN:
if not in_transposition:
diff --git a/mutalyzer/extractor_loader.py b/mutalyzer/extractor_loader.py
index c1930c3a..81f43cce 100644
--- a/mutalyzer/extractor_loader.py
+++ b/mutalyzer/extractor_loader.py
@@ -25,9 +25,9 @@ def main():
extracted_allele = describe.describe_dna(ref, alt)
- print "Description Extractor Version " + 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)
+ #print "Description Extractor Version " + describe.extractor.VERSION
+ print extracted_allele
+ #print "JSON: " + json.dumps({"reference_sequence": ref, "sample_sequence": alt, "allele_description": extracted_allele}, cls=MyEncoder)
#main
diff --git a/mutalyzer/test.py b/mutalyzer/test.py
index 3bd46d1a..acdca95d 100644
--- a/mutalyzer/test.py
+++ b/mutalyzer/test.py
@@ -15,7 +15,6 @@ def main():
extracted_allele = describe.describe_dna(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
--
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