From bcef1633716c3661678d9b5b864da9f98625e3c9 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Wed, 15 Oct 2014 10:53:33 +0200
Subject: [PATCH] Fix several error cases in LOVD2 getGS call
The `getGS` website view for LOVD2 would report "transcript not found" if
the genomic reference has multiple transcripts annotated or if the variant
description raises an error in the variant checker.
---
mutalyzer/variantchecker.py | 32 ++++++++++++++++----------------
tests/test_website.py | 28 ++++++++++++++++++++++++++++
2 files changed, 44 insertions(+), 16 deletions(-)
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index aabac6e0..65dd7056 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -1702,22 +1702,6 @@ def check_variant(description, output):
record = GenRecord.GenRecord(output)
record.record = retrieved_record
- # Note: The GenRecord instance is carrying the sequence in .record.seq.
- # So is the Mutator instance in .mutator.orig.
-
- mutator = Mutator(record.record.seq, output)
-
- # Todo: If processing of the variant fails, we might still want to show
- # information about the record, gene, transcript.
-
- try:
- process_variant(mutator, parsed_description, record, output)
- except _VariantError:
- return
-
- output.addOutput('original', str(mutator.orig))
- output.addOutput('mutated', str(mutator.mutated))
-
# Create the legend.
for gene in record.record.geneList:
for transcript in sorted(gene.transcriptList, key=attrgetter('name')):
@@ -1735,6 +1719,22 @@ def check_variant(description, output):
transcript.proteinProduct,
transcript.linkMethod])
+ # Note: The GenRecord instance is carrying the sequence in .record.seq.
+ # So is the Mutator instance in .mutator.orig.
+
+ mutator = Mutator(record.record.seq, output)
+
+ # Todo: If processing of the variant fails, we might still want to show
+ # information about the record, gene, transcript.
+
+ try:
+ process_variant(mutator, parsed_description, record, output)
+ except _VariantError:
+ return
+
+ output.addOutput('original', str(mutator.orig))
+ output.addOutput('mutated', str(mutator.mutated))
+
# Chromosomal region (only for GenBank human transcript references).
# This is still quite ugly code, and should be cleaned up once we have
# a refactored mapping module.
diff --git a/tests/test_website.py b/tests/test_website.py
index 44d9e996..e579433a 100644
--- a/tests/test_website.py
+++ b/tests/test_website.py
@@ -553,6 +553,34 @@ class TestWebsite(MutalyzerTest):
assert 'go to bottom' not in r.data
assert '<input' not in r.data
+ @fix(database, cache('NG_012337.1'))
+ def test_getgs_coding_multiple_transcripts(self):
+ """
+ Test the /getGS interface on a coding description and genomic
+ reference with multiple transcripts.
+ """
+ r = self.app.get('/getGS',
+ query_string={'variantRecord': 'NM_003002.2',
+ 'forward': '1',
+ 'mutationName': 'NG_012337.1:c.45A>T'},
+ follow_redirects=False)
+ assert '/name-checker?' in r.location
+ assert 'description=NG_012337.1' in r.location
+
+ @fix(database, cache('NG_008939.1'))
+ def test_getgs_variant_error(self):
+ """
+ Test the /getGS interface on a variant description with an error.
+ """
+ # The error is that position c.45 is a C, not an A.
+ r = self.app.get('/getGS',
+ query_string={'variantRecord': 'NM_000532.4',
+ 'forward': '1',
+ 'mutationName': 'NG_008939.1:c.45A>T'},
+ follow_redirects=False)
+ assert '/name-checker?' in r.location
+ assert 'description=NG_008939.1' in r.location
+
@fix(database, hg19, hg19_transcript_mappings)
def test_variantinfo_g2c(self):
"""
--
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