From ba9a6a5cbc0219d353a08a4661fbb90ca5f5893b Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Thu, 16 Jan 2014 23:09:42 +0100
Subject: [PATCH] Fix bug in position converter for chrM
---
mutalyzer/mapping.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index 7bc9813b..cec62b63 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -160,12 +160,13 @@ class Converter(object) :
if version in versions:
mappings = TranscriptMapping.query.join(Chromosome).filter(
- TranscriptMapping.accession == acc, TranscriptMapping.version == version,
+ TranscriptMapping.accession == acc,
+ TranscriptMapping.version == version,
Chromosome.assembly == self.assembly)
if selector:
- mappings = mappings.filter_by(gene=selector)
+ mappings = mappings.filter(TranscriptMapping.gene == selector)
if selector_version:
- mappings = mappings.filter_by(transcript=selector_version)
+ mappings = mappings.filter(TranscriptMapping.transcript == selector_version)
# Todo: The 'order by chrom asc' is a quick hack to make sure we
# first get a primary assembly mapping instead of some haplotype
--
GitLab