From abcc94605d700ef3e854d658f75ead781905bb0c Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Tue, 12 Apr 2011 13:20:00 +0000
Subject: [PATCH] Small fixes.
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@268 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
extras/soap-tools/namecheck.py | 2 +-
mutalyzer/File.py | 7 +++----
mutalyzer/GenRecord.py | 20 ++++++++++++--------
mutalyzer/variantchecker.py | 23 ++++++++++++-----------
4 files changed, 28 insertions(+), 24 deletions(-)
diff --git a/extras/soap-tools/namecheck.py b/extras/soap-tools/namecheck.py
index 6aa47f1e..c0f48524 100755
--- a/extras/soap-tools/namecheck.py
+++ b/extras/soap-tools/namecheck.py
@@ -15,7 +15,7 @@
import sys
from suds.client import Client # https://fedorahosted.org/suds/
-VERBOSE = True
+VERBOSE = False
URL = 'http://localhost/mutalyzer/services/?wsdl'
diff --git a/mutalyzer/File.py b/mutalyzer/File.py
index 7bfd479d..fd2e892b 100644
--- a/mutalyzer/File.py
+++ b/mutalyzer/File.py
@@ -378,10 +378,9 @@ class File() :
#allow a 5 (default) percent threshold for errors in batchfiles
self.__output.addMessage(__file__, 3, "EBPARSE",
"There were errors in your batch entry file, they are "
- "omitted and your batch is started.")
- self.__output.addMessage(__file__, 3, "EBPARSE",
- "Please check the batch input file help at the top of "
- "this page for additional information.")
+ "omitted and your batch is started. Please check the "
+ "batch input file help at the top of this page for "
+ "additional information.")
return (ret, columns)
else:
return (None, columns)
diff --git a/mutalyzer/GenRecord.py b/mutalyzer/GenRecord.py
index d66c3194..fedf5d32 100644
--- a/mutalyzer/GenRecord.py
+++ b/mutalyzer/GenRecord.py
@@ -1,5 +1,3 @@
-#!/usr/bin/python
-
"""
Module to convert a GenBank record to a nested dictionary consisting of
a list of genes, which itself consists of a list of loci. This structure
@@ -89,6 +87,7 @@ class Locus(object) :
"""
self.name = name
+ self.current = False
self.mRNA = None
self.CDS = None
self.location = []
@@ -646,12 +645,22 @@ class GenRecord() :
orientedStop = reverseStop
#if
- # Check whether the variant hits CDS start.
+ # Turn of translation to protein if we hit splice sites.
+ # For the current transcript, this is handled with more
+ # care in variantchecker.py.
+ if not j.current and \
+ util.over_splice_site(orientedStart, orientedStop,
+ j.CM.RNA):
+ j.translate = False
+
+ # And check whether the variant hits CDS start.
if j.molType == 'c' and forwardStop >= j.CM.x2g(1, 0) \
and forwardStart <= j.CM.x2g(3, 0) :
self.__output.addMessage(__file__, 2, "WSTART",
"Mutation in start codon of gene %s transcript " \
"%s." % (i.name, j.name))
+ if not j.current:
+ j.translate = False
# FIXME Check whether the variant hits a splice site.
@@ -713,8 +722,3 @@ class GenRecord() :
#if
#checkIntron
#GenRecord
-
-if __name__ == "__main__" :
- R = GenRecord()
- del R
-#if
diff --git a/mutalyzer/variantchecker.py b/mutalyzer/variantchecker.py
index 909906e0..52d1fd46 100644
--- a/mutalyzer/variantchecker.py
+++ b/mutalyzer/variantchecker.py
@@ -363,6 +363,8 @@ def apply_deletion_duplication(first, last, type, mutator, record, O):
mutator.visualiseLargeString(str(mutator.orig[incorrect_first - 1:incorrect_stop])),
util.format_range(incorrect_first, incorrect_stop)))
+ # Todo: I think we should use shifted first and last here...
+ # Likewise for other apply_* functions.
if type == 'del':
mutator.delM(first, last)
else :
@@ -914,15 +916,11 @@ def process_raw_variant(mutator, variant, record, transcript, output):
# If we hit a splice site, issue a warning. Later on we decide if we
# can still process this variant in any way (e.g. if it deletes an
# entire exon).
- for gene in record.record.geneList:
- for t in gene.transcriptList:
- if t.CM and util.over_splice_site(first, last, t.CM.RNA):
- if t == transcript:
- splice_abort = True
- output.addMessage(__file__, 2, 'WOVERSPLICE',
- 'Variant hits one or more splice sites.')
- else:
- t.translate = False
+ if transcript and util.over_splice_site(first, last, transcript.CM.RNA):
+ splice_abort = True
+ output.addMessage(__file__, 2, 'WOVERSPLICE',
+ 'Variant hits one or more splice sites in ' \
+ 'selected transcript.')
# If we have a deletion, and it covers exactly an even number of splice
# sites, remove these splice sites.
@@ -954,8 +952,8 @@ def process_raw_variant(mutator, variant, record, transcript, output):
splice_abort = False
mutator.add_removed_sites(removed_sites)
output.addMessage(__file__, 1, 'IDELSPLICE',
- 'Removed %i splice sites from transcript.' \
- % len(removed_sites))
+ 'Removed %i splice sites from selected ' \
+ 'transcript.' % len(removed_sites))
# If splice_abort is set, this basically means WOVERSPLICE was called and
# IDELSPLICE was not called.
@@ -1231,6 +1229,9 @@ def process_variant(mutator, description, record, output):
# Todo: Shouldn't we add some message here?
raise _VariantError()
+ # Mark this as the current transcript we work with.
+ transcript.current = True
+
# Add static transcript-specific information.
if transcript and record.record.geneList:
_add_static_transcript_info(transcript, output)
--
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