def checkUndirectedEdges(genome, trackName, allowOverlaps):
collector = PreProcMetaDataCollector(genome, trackName)
if not (collector.getTrackFormat().isLinked() and collector.hasUndirectedEdges()):
return
complementEdgeWeightDict = {}
for chr in collector.getPreProcessedChrs(allowOverlaps):
trackSource = TrackSource()
trackData = trackSource.getTrackData(trackName, genome, chr, allowOverlaps)
ids = trackData['id']
edges = trackData['edges']
weights = trackData.get('weights')
for i, id in enumerate(ids):
edgesAttr = edges[i][edges[i] != '']
weightsAttr = weights[i][edges[i] != ''] if weights is not None else None
PreProcessUtils._adjustComplementaryEdgeWeightDict(complementEdgeWeightDict, id, edgesAttr, weightsAttr)
if len(complementEdgeWeightDict) != 0:
unmatchedPairs = []
for toId in complementEdgeWeightDict:
for fromId in complementEdgeWeightDict[toId]:
unmatchedPairs.append((fromId, toId, complementEdgeWeightDict[toId][fromId]))
raise InvalidFormatError("Error: All edges are not undirected. The following edges specifications " +\
"are not matched by an opposite edge with equal weight:" + os.linesep +\
os.linesep.join(["from '%s' to '%s'" % (fromId, toId) + \
(" with weight '%s'" % weight if weight != '' else '') \
for fromId, toId, weight in unmatchedPairs]))
def _findTrackInfoBasedMetaData(self):
if not self._foundTrackInfoBasedMetaData:
if PreProcMetaDataCollector.hasKey(self._genome, self._trackName):
collector = PreProcMetaDataCollector(self._genome, self._trackName)
self._fileSuffix = collector.getFileSuffix()
self._geSourceVersion = collector.getGeSourceVersion()
self._id = collector.getId()
self._undirectedEdges = True if collector.hasUndirectedEdges() else False
else:
ti = TrackInfo(self._genome, self._trackName)
self._fileSuffix = ti.fileType
self._geSourceVersion = ti.geSourceVersion
self._id = ti.id
self._undirectedEdges = True if ti.undirectedEdges else False