Commit 0148a9fc authored by Alisa Muraveva's avatar Alisa Muraveva
Browse files

Look only ENS***... genes (but not ENSEST...). And file in *.embl format

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@727 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
parent 6a8df824
......@@ -538,26 +538,28 @@ class EMBLparser():
if i.qualifiers.has_key("gene") :
geneName = i.qualifiers["gene"][0]
if i.type == "gene" :
if not geneDict.has_key(geneName) :
myGene = Gene(geneName)
record.geneList.append(myGene)
if i.strand :
myGene.orientation = i.strand
myGene.location = self.__location2pos(i.location)
geneDict[geneName] = tempGene(geneName)
if geneName.startswith('ENS') and geneName[3:6] != 'EST':
if i.type == "gene" :
if not geneDict.has_key(geneName) :
myGene = Gene(geneName)
record.geneList.append(myGene)
if i.strand :
myGene.orientation = i.strand
myGene.location = self.__location2pos(i.location)
geneDict[geneName] = tempGene(geneName)
#if
#if
#if
if i.type in ["mRNA", "misc_RNA", "ncRNA", "rRNA", "tRNA",
"tmRNA"] :
geneDict[geneName].rnaList.append(i)
if i.type == "CDS" :
geneDict[geneName].cdsList.append(i)
if i.type == "exon" :
exonLocation = self.__location2pos(i.location)
if exonLocation :
exonList.extend(exonLocation)
if i.type in ["mRNA", "misc_RNA", "ncRNA", "rRNA", "tRNA",
"tmRNA"] :
geneDict[geneName].rnaList.append(i)
if i.type == "CDS" :
geneDict[geneName].cdsList.append(i)
if i.type == "exon" :
exonLocation = self.__location2pos(i.location)
if exonLocation :
exonList.extend(exonLocation)
#if
#if
#if
......
......@@ -1666,6 +1666,12 @@ def check_variant(description, output):
retriever = Retriever.LRGRetriever(output, database)
elif parsed_description.EnsemblId:
filetype = 'EMBL'
if parsed_description.Gene:
gene_symbol = parsed_description.Gene.GeneSymbol or ''
transcript_id = parsed_description.Gene.TransVar or ''
if parsed_description.Gene.ProtIso:
output.addMessage(__file__, 4, 'EPROT',
'Indexing by protein isoform is not supported.')
retriever = Retriever.EMBLRetriever(output, database)
else:
......
......@@ -819,6 +819,8 @@ class Check:
if reference:
if record_type == 'LRG':
reference = reference + '.xml'
elif record_type == 'EMBL':
reference = reference + '.embl'
else :
reference = reference + '.gb'
......
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