From 1376c5249e40533837cd19805587439a1d044a36 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Thu, 1 Mar 2012 12:54:59 +0000
Subject: [PATCH] Fix CDS start and stop in mapping database
During import of the NCBI transcript mappings, CDS start or stop positions
were not picked up for some transcripts (where these are on exon boundaries).
Bug reported by S Venkata Suresh Kumar.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@490 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
extras/cron.d/mutalyzer-mapping-update | 2 +-
mutalyzer/Db.py | 2 +-
mutalyzer/mapping.py | 15 ++++++---------
tests/test_mapping.py | 16 ++++++++++++++++
4 files changed, 24 insertions(+), 11 deletions(-)
diff --git a/extras/cron.d/mutalyzer-mapping-update b/extras/cron.d/mutalyzer-mapping-update
index cac1a976..496571df 100644
--- a/extras/cron.d/mutalyzer-mapping-update
+++ b/extras/cron.d/mutalyzer-mapping-update
@@ -2,4 +2,4 @@
#25 3 * * 7 www-data wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md; <MUTALYZER_BIN_MAPPING_UPDATE> hg18 /tmp/seq_gene.md reference
#25 4 * * 7 www-data wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.37.2/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md; <MUTALYZER_BIN_MAPPING_UPDATE> hg19 /tmp/seq_gene.md 'GRCh37.p2-Primary Assembly'
-##25 4 * * 7 www-data wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md; <MUTALYZER_BIN_MAPPING_UPDATE> hg19 /tmp/seq_gene.md 'GRCh37.p2-Primary Assembly'
+##25 4 * * 7 www-data wget "ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/mapview/seq_gene.md.gz" -O - | zcat > /tmp/seq_gene.md; <MUTALYZER_BIN_MAPPING_UPDATE> hg19 /tmp/seq_gene.md 'GRCh37.p5-Primary Assembly'
diff --git a/mutalyzer/Db.py b/mutalyzer/Db.py
index bc6c7625..b8a6ff9c 100644
--- a/mutalyzer/Db.py
+++ b/mutalyzer/Db.py
@@ -644,7 +644,7 @@ class Mapping(Db) :
T.orientation as orientation,
MIN(T.start) as start,
MAX(T.stop) as stop,
- MAX(E.cds_start) as cds_start,
+ REPLACE(MIN(COALESCE(E.cds_start, 1000000000)), 1000000000, NULL) as cds_start,
MAX(E.cds_stop) as cds_stop,
GROUP_CONCAT(DISTINCT E.start ORDER BY E.start ASC) as exon_starts,
GROUP_CONCAT(DISTINCT E.stop ORDER BY E.stop ASC) as exon_stops,
diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py
index 3c70668d..d93ff17e 100644
--- a/mutalyzer/mapping.py
+++ b/mutalyzer/mapping.py
@@ -833,6 +833,8 @@ class NCBIUpdater(Updater):
entry['start'] = int(entry['start'])
entry['stop'] = int(entry['stop'])
entry['protein'] = entry['feature_name'] if cds else None
+ entry['cds_start'] = entry['start'] if cds else None
+ entry['cds_stop'] = entry['stop'] if cds else None
entry['cds'] = cds
self._import_exon_backlog(entry['start'] - 1)
@@ -841,12 +843,9 @@ class NCBIUpdater(Updater):
previous = self.exon_backlog[entry['transcript']]
if previous['cds'] != entry['cds'] \
and previous['stop'] == entry['start'] - 1:
- if entry['cds']:
- entry['cds_start'] = entry['start']
- else:
- entry['cds_stop'] = previous['stop']
- if 'cds_start' in previous:
- entry['cds_start'] = previous['cds_start']
+ if previous['cds']:
+ entry['cds_start'] = previous['cds_start']
+ entry['cds_stop'] = previous['cds_stop']
entry['protein'] = previous['protein']
entry['start'] = previous['start']
except KeyError:
@@ -870,9 +869,7 @@ class NCBIUpdater(Updater):
del exon['cds']
self.db.ncbi_import_exon(
exon['transcript'], exon['chromosome'], exon['start'], exon['stop'],
- exon['cds_start'] if 'cds_start' in exon else None,
- exon['cds_stop'] if 'cds_stop' in exon else None,
- exon['protein'] or None)
+ exon['cds_start'], exon['cds_stop'], exon['protein'] or None)
#_import_exon_backlog
def _aggregate_mapping(self):
diff --git a/tests/test_mapping.py b/tests/test_mapping.py
index 3180d521..72a21f3c 100644
--- a/tests/test_mapping.py
+++ b/tests/test_mapping.py
@@ -60,3 +60,19 @@ class TestConverter():
coding = converter.chrom2c('NC_000022.10:g.51016285_51017117del123456789', 'list')
assert 'NM_001145134.1:c.-138-u21_60del123456789' in coding
assert 'NR_021492.1:c.1-u5170_1-u4338del123456789' in coding
+
+ def test_S_Venkata_Suresh_Kumar(self):
+ """
+ Test for correct mapping information on genes where CDS start or stop
+ is exactly on the border of an exon.
+
+ Bug reported February 24 by S Venkata Suresh Kumartest.
+ """
+ converter = self._converter('hg19')
+ coding = converter.chrom2c('NC_000001.10:g.115259837_115259837delT', 'list')
+ assert 'NM_001007553.1:c.3863delA' not in coding
+ assert 'NM_001007553.2:c.3863delA' not in coding
+ assert 'NM_001007553.1:c.*953delA' in coding
+ assert 'NM_001130523.1:c.*953delA' in coding
+ assert 'NM_001007553.2:c.*953delA' in coding
+ assert 'NM_001130523.2:c.*953delA' in coding
--
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