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

@@ -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}
 

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:])

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

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