From 0c5f32eaff8b97626f0772cd8582baf57266640e Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 31 Jan 2012 15:02:01 +0000
Subject: [PATCH] Describe NOP variants with = (#88)
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@472 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/variantchecker.py | 8 ++++----
tests/test_variantchecker.py | 31 +++++++++++++++++++++++++++++++
tests/test_webservice.py | 5 +++++
3 files changed, 40 insertions(+), 4 deletions(-)
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index d0b5faef..7b5dc5ed 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -1223,7 +1223,7 @@ def _add_transcript_info(mutator, transcript, output):
"""
# Add transcript info to output.
if transcript.transcribe:
- output.addOutput('myTranscriptDescription', transcript.description)
+ output.addOutput('myTranscriptDescription', transcript.description or '=')
output.addOutput('origMRNA',
str(util.splice(mutator.orig, transcript.mRNA.positionList)))
output.addOutput('mutatedMRNA',
@@ -1661,7 +1661,7 @@ def check_variant(description, output):
if ';' in record.record.description:
generated_description = '[' + record.record.description + ']'
else:
- generated_description = record.record.description
+ generated_description = record.record.description or '='
output.addOutput('genomicDescription', '%s:%c.%s' % \
(reference, record.record.molType, generated_description))
@@ -1673,7 +1673,7 @@ def check_variant(description, output):
if ';' in record.record.chromDescription:
chromosomal_description = '[' + record.record.chromDescription + ']'
else:
- chromosomal_description = record.record.chromDescription
+ chromosomal_description = record.record.chromDescription or '='
output.addOutput('genomicChromDescription', '%s:%c.%s' % \
(record.record.recordId,
record.record.molType, chromosomal_description))
@@ -1694,7 +1694,7 @@ def check_variant(description, output):
if ';' in transcript.description:
generated_description = '[' + transcript.description + ']'
else:
- generated_description = transcript.description
+ generated_description = transcript.description or '='
if record.record._sourcetype == 'LRG':
if transcript.name:
diff --git a/tests/test_variantchecker.py b/tests/test_variantchecker.py
index 65d5c45c..f5ae5034 100644
--- a/tests/test_variantchecker.py
+++ b/tests/test_variantchecker.py
@@ -6,6 +6,7 @@ Tests for the variantchecker module.
#import logging; logging.basicConfig()
from nose.tools import *
+from mutalyzer.util import skip
from mutalyzer.output import Output
from mutalyzer.variantchecker import check_variant
@@ -496,3 +497,33 @@ class TestVariantchecker():
'31317229:n.105del')
assert '31317229(FCER1A_v001):c.6del' \
in self.output.getOutput('descriptions')
+
+ def test_nop_nm(self):
+ """
+ Variant on NM without effect should be described as '='.
+ """
+ check_variant('NM_002001.2:c.1_3delinsATG', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'NM_002001.2:n.=')
+ assert 'NM_002001.2(FCER1A_v001):c.=' \
+ in self.output.getOutput('descriptions')
+
+ @skip
+ def test_nop_ud(self):
+ """
+ Variant on UD without effect should be described as '='.
+
+ Todo: We cannot use UD references in unit tests, unless we implement
+ a way to create them inside the unit test.
+ """
+ check_variant('UD_127955523176:g.5T>T', self.output)
+ error_count, _, _ = self.output.Summary()
+ assert_equal(error_count, 0)
+ assert_equal(self.output.getIndexedOutput('genomicChromDescription', 0),
+ 'NC_000023.10:g.=')
+ assert_equal(self.output.getIndexedOutput('genomicDescription', 0),
+ 'UD_127955523176:g.=')
+ assert 'UD_127955523176(DMD_v001):c.=' \
+ in self.output.getOutput('descriptions')
diff --git a/tests/test_webservice.py b/tests/test_webservice.py
index 7d179e6f..f50ecc3e 100644
--- a/tests/test_webservice.py
+++ b/tests/test_webservice.py
@@ -8,6 +8,7 @@ from mutalyzer.util import monkey_patch_suds; monkey_patch_suds()
import os
from datetime import datetime, timedelta
import mutalyzer
+from mutalyzer.util import skip
from mutalyzer.output import Output
from mutalyzer.sync import CacheSync
from mutalyzer import Db
@@ -334,9 +335,13 @@ class TestWebservice():
assert_equal(r.sourceGi, '222352156')
assert_equal(r.molecule, 'n')
+ @skip
def test_runmutalyzer_reference_info_ud(self):
"""
Get reference info for a UD variant.
+
+ Todo: We cannot use UD references in unit tests, unless we implement
+ a way to create them inside the unit test.
"""
r = self.client.service.runMutalyzer('UD_129433404385:g.1del')
assert_equal(r.errors, 0)
--
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