From 1b5d48b300c9b9262d9e23549aad267154e62d31 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 8 May 2012 07:57:07 +0000
Subject: [PATCH] Use WSPLICESELECTED for selected transcript (WSPLICE
otherwise).
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@518 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
mutalyzer/GenRecord.py | 35 ++++++++++++++++++-----------------
1 file changed, 18 insertions(+), 17 deletions(-)
diff --git a/mutalyzer/GenRecord.py b/mutalyzer/GenRecord.py
index f4a8ad2a..d06547ab 100644
--- a/mutalyzer/GenRecord.py
+++ b/mutalyzer/GenRecord.py
@@ -807,7 +807,7 @@ class GenRecord() :
#for
#name
- def checkIntron(self, gene, transcript, position) :
+ def checkIntron(self, gene, transcript, position):
"""
Checks if a position is on or near a splice site
@@ -817,25 +817,26 @@ class GenRecord() :
@type transcript: object
@arg position: g. position
@type position: integer
-
- @return:
- @todo: Also check a range properly.
"""
- # TODO Also check a range properly.
intronPos = abs(transcript.CM.g2x(position)[1])
+
if intronPos :
+ # It should be easy for SOAP clients to filter out all warnings
+ # related to other transcripts, so we use two codes here.
+ if transcript.current:
+ warning = 'WSPLICESELECTED'
+ str_transcript = 'transcript %s (selected)' % transcript.name
+ else:
+ warning = 'WSPLICE'
+ str_transcript = 'transcript %s' % transcript.name
+
if intronPos <= config.get('spliceAlarm'):
- self.__output.addMessage(__file__, 2, "WSPLICE",
- "Mutation on splice site in gene %s transcript %s." % (
- gene.name, transcript.name))
- return
- #if
- if intronPos <= config.get('spliceWarn'):
- self.__output.addMessage(__file__, 2, "WSPLICE",
- "Mutation near splice site in gene %s transcript %s." % (
- gene.name, transcript.name))
- return
- #if
- #if
+ self.__output.addMessage(__file__, 2, warning,
+ "Mutation on splice site in gene %s %s." % (
+ gene.name, str_transcript))
+ elif intronPos <= config.get('spliceWarn'):
+ self.__output.addMessage(__file__, 2, warning,
+ "Mutation near splice site in gene %s %s." % (
+ gene.name, str_transcript))
#checkIntron
#GenRecord
--
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