From 216146bbbc90222ef2c9b6685a7aa5b76db177f6 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Fri, 27 Mar 2015 18:22:09 +0100
Subject: [PATCH] Integrated the description extractor in the website.
---
mutalyzer/variant.py | 3 +++
mutalyzer/website/views.py | 18 +++++++++++-------
tests/test_describe.py | 2 +-
3 files changed, 15 insertions(+), 8 deletions(-)
diff --git a/mutalyzer/variant.py b/mutalyzer/variant.py
index 33ffc258..a8e512a2 100644
--- a/mutalyzer/variant.py
+++ b/mutalyzer/variant.py
@@ -70,6 +70,9 @@ class ISeq(object):
if self.type == "ins":
return self.sequence
+ if not (self.start or self.end):
+ return ""
+
inverted = "inv" if self.reverse else ""
return "{}_{}{}".format(self.start, self.end, inverted)
#__str__
diff --git a/mutalyzer/website/views.py b/mutalyzer/website/views.py
index c1d761c4..5bb2ae35 100644
--- a/mutalyzer/website/views.py
+++ b/mutalyzer/website/views.py
@@ -269,14 +269,18 @@ def name_checker():
# Experimental description extractor.
if (output.getIndexedOutput('original', 0) and
output.getIndexedOutput('mutated', 0)):
- extracted = extractedProt = '(skipped)'
+ allele = describe.describe_dna(output.getIndexedOutput('original', 0),
+ output.getIndexedOutput('mutated', 0))
+ #prot_allele = describe.describe_protein(
+ # output.getIndexedOutput('oldprotein', 0),
+ # output.getIndexedOutput('newprotein', 0, default=''))
+ prot_allele = ''
- allele = describe.describe(output.getIndexedOutput('original', 0),
- output.getIndexedOutput('mutated', 0))
+ extracted = extractedProt = '(skipped)'
if allele:
- extracted = describe.allele_description(allele)
+ extracted = str(allele) #describe.allele_description(allele)
if prot_allele:
- extractedProt = describe.allele_description(prot_allele)
+ extractedProt = str(prot_allele) #describe.allele_description(prot_allele)
else:
extracted = extractedProt = ''
@@ -695,8 +699,8 @@ def description_extractor():
output.addMessage(__file__, 3, 'ENODNA',
'Variant sequence is not DNA.')
- raw_vars = describe.describe(reference_sequence, variant_sequence)
- description = describe.allele_description(raw_vars)
+ raw_vars = describe.describe_dna(reference_sequence, variant_sequence)
+ description = str(raw_vars) #describe.allele_description(raw_vars)
errors, warnings, summary = output.Summary()
messages = map(util.message_info, output.getMessages())
diff --git a/tests/test_describe.py b/tests/test_describe.py
index 2ef7db3d..c65e57a5 100644
--- a/tests/test_describe.py
+++ b/tests/test_describe.py
@@ -16,7 +16,7 @@ from utils import MutalyzerTest
class TestDescribe(MutalyzerTest):
"""
- Test the mytalyzer.describe module.
+ Test the mutalyzer.describe module.
"""
def _single_variant(self, sample, expected):
--
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