class VariantsGffWriter(object):
ONTOLOGY_URL = \
"http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12"
def __init__(self, f, optionsDict, referenceEntries):
self._gffWriter = GffWriter(f)
self._gffWriter.writeHeader("##pacbio-variant-version 2.1")
self._gffWriter.writeHeader("##date %s" % time.ctime())
self._gffWriter.writeHeader("##feature-ontology %s" %
self.ONTOLOGY_URL)
self._gffWriter.writeHeader("##source GenomicConsensus %s" %
__VERSION__)
self._gffWriter.writeHeader("##source-commandline %s" %
optionsDict["shellCommand"])
self._gffWriter.writeHeader("##source-alignment-file %s" %
optionsDict["inputFilename"])
self._gffWriter.writeHeader("##source-reference-file %s" %
optionsDict["referenceFilename"])
# Reference groups.
for entry in referenceEntries:
self._gffWriter.writeHeader("##sequence-region %s 1 %d" \
% (entry.name, entry.length))
def writeVariants(self, variants):
for var in variants:
self._gffWriter.writeRecord(toGffRecord(var))
def close(self):
self._gffWriter.close()
class VariantsGffWriter(object):
ONTOLOGY_URL = \
"http://song.cvs.sourceforge.net/*checkout*/song/ontology/sofa.obo?revision=1.12"
def __init__(self, f, optionsDict, referenceEntries):
self._gffWriter = GffWriter(f)
self._minConfidence = optionsDict["minConfidence"]
self._minCoverage = optionsDict["minCoverage"]
self._gffWriter.writeHeader("##pacbio-variant-version 2.1")
self._gffWriter.writeHeader("##date %s" % time.ctime())
self._gffWriter.writeHeader("##feature-ontology %s" % self.ONTOLOGY_URL)
self._gffWriter.writeHeader("##source GenomicConsensus %s" % __VERSION__)
self._gffWriter.writeHeader("##source-commandline %s" % optionsDict["shellCommand"])
self._gffWriter.writeHeader("##source-alignment-file %s" % optionsDict["inputFilename"])
self._gffWriter.writeHeader("##source-reference-file %s" % optionsDict["referenceFilename"])
# Reference groups.
for entry in referenceEntries:
self._gffWriter.writeHeader("##sequence-region %s 1 %d" \
% (entry.name, entry.length))
def writeVariants(self, variants):
for var in variants:
if var.coverage >= self._minCoverage and var.confidence >= self._minConfidence:
self._gffWriter.writeRecord(toGffRecord(var))
def close(self):
self._gffWriter.close()
