From 407fbe2bf8b03eacc75ef60f872617fa4455a809 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <j.f.j.laros@lumc.nl>
Date: Fri, 3 Sep 2010 12:31:10 +0000
Subject: [PATCH] Mutalyzer.py: - Made the ``multiple transcripts found''
message more descriptive. - Made the ``in frame stop codon'' check work for
all organisms (and organelles).
GBparser.py:
- Added mitochondrial DNA to the list of possible molecular types to be
checked, it will be treated like genomic DNA.
- Allowed genes without CDS list or mRNA list (only a CDS location) as a
genomic description only if there are no other CDS's for that gene.
GenRecord.py:
- Fixed a bug in the naming of the link method (it should also apply when mRNA
is constructed from a CDS location only).
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@87 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
---
doc/TechnicalReference/TechnicalReference.tex | 2 +-
src/Modules/GBparser.py | 5 +++--
src/Modules/GenRecord.py | 2 +-
src/Mutalyzer.py | 6 +++---
4 files changed, 8 insertions(+), 7 deletions(-)
diff --git a/doc/TechnicalReference/TechnicalReference.tex b/doc/TechnicalReference/TechnicalReference.tex
index 6a8eb499..b81aa6a5 100644
--- a/doc/TechnicalReference/TechnicalReference.tex
+++ b/doc/TechnicalReference/TechnicalReference.tex
@@ -780,7 +780,7 @@ returned by the \texttt{\_\_toProtDescr()} function as described in
Section~\ref{subsubsec:effect}.
\subsection{VarInfo} \label{subsec:varinfo}
-
+The VarInfo interface is a (soon to be deprecated) interface for LOVD~\cite{LOVDD}
\subsection{UCSC\_Update} \label{subsec:ucsc_update}
diff --git a/src/Modules/GBparser.py b/src/Modules/GBparser.py
index a2c3ccdb..4f8988f8 100644
--- a/src/Modules/GBparser.py
+++ b/src/Modules/GBparser.py
@@ -481,7 +481,7 @@ class GBparser() :
#if
#if
#for
- if record.molType == 'g' :
+ if record.molType in ['g', 'm'] :
for j in geneDict.keys() :
myGene = geneDict[j]
self.link(myGene.rnaList, myGene.cdsList)
@@ -515,7 +515,8 @@ class GBparser() :
#if
#for
for i in myGene.cdsList :
- if not i.linked and i.usable :
+ if not i.linked and \
+ (i.usable or not geneDict[myGene.name].rnaList) :
myRealGene = record.findGene(i.gene)
if i.locus_tag :
myTranscript = Locus(i.locus_tag[-3:])
diff --git a/src/Modules/GenRecord.py b/src/Modules/GenRecord.py
index 8f8a3a86..36707803 100644
--- a/src/Modules/GenRecord.py
+++ b/src/Modules/GenRecord.py
@@ -379,7 +379,7 @@ class GenRecord() :
#if
else :
j.mRNA = j.CDS
- j.linkMethod = "construction"
+ j.linkMethod = "construction"
j.transcribe = True
j.translate = True
#if
diff --git a/src/Mutalyzer.py b/src/Mutalyzer.py
index e2a72344..0ad6fb85 100644
--- a/src/Mutalyzer.py
+++ b/src/Mutalyzer.py
@@ -1158,7 +1158,7 @@ def __ppp(MUU, parts, GenRecordInstance, O) :
W = GS.findLocus(toi)
if not W:
O.addMessage(__file__, 4, "ENOTRANSCRIPT",
- "Transcripts found for gene %s. Please " \
+ "Multiple transcripts found for gene %s. Please " \
"choose from: %s" %(GS.name,
", ".join(GS.listLoci())))
else: # No transcript id given
@@ -1196,7 +1196,7 @@ def __ppp(MUU, parts, GenRecordInstance, O) :
W = GS.transcriptList[0]
else:
O.addMessage(__file__, 4, "ENOTRANSCRIPT",
- "Transcripts found for gene %s. Please " \
+ "Multiple transcripts found for gene %s. Please " \
"choose from: %s" %(GS.name,
", ".join(GS.listLoci())))
#else
@@ -1258,7 +1258,7 @@ def __ppp(MUU, parts, GenRecordInstance, O) :
cdsm = Bio.Seq.reverse_complement(cdsm)
#if
- if '*' in cds.translate()[:-1] :
+ if '*' in cds.translate(table = W.txTable)[:-1] :
O.addMessage(__file__, 3, "ESTOP", "In frame stop codon found.")
return
#if
--
GitLab