def _commonComplementGtrackFile(origFn, dbFn, intersectingFactor, gtrackColsToAdd, genome):
origGESource = GtrackGenomeElementSource(origFn, genome)
dbGESource = GtrackGenomeElementSource(dbFn, genome)
dbPrefixes = dbGESource.getPrefixList()
if intersectingFactor == 'id':
fullDbDict = IdFullInfoDict(dbGESource, dbPrefixes)
elif intersectingFactor == 'position':
fullDbDict = TupleFullInfoDict(dbGESource, dbPrefixes)
else:
ShouldNotOccurError
forcedHeaderDict = {}
dbHeaderDict = dbGESource.getHeaderDict()
if 'value' in gtrackColsToAdd:
forcedHeaderDict['value type'] = dbHeaderDict['value type']
forcedHeaderDict['value dimension'] = dbHeaderDict['value dimension']
if 'edges' in gtrackColsToAdd:
forcedHeaderDict['edge weight type'] = dbHeaderDict['edge weight type']
forcedHeaderDict['edge weight dimension'] = dbHeaderDict['edge weight dimension']
composerCls = ExtendedGtrackComposer if origGESource.isExtendedGtrackFile() else StdGtrackComposer
composedFile = composerCls( ElementComplementer(origGESource, fullDbDict, gtrackColsToAdd), \
forcedHeaderDict=forcedHeaderDict).returnComposed()
return expandHeadersOfGtrackFileAndReturnComposer('', genome, strToUseInsteadOfFn=composedFile)
def _determineIfFileCompliesToSubtypes(self, hbColumns, columns):
if "subtype url" in self._forcedHeaderDict:
subtypeUrlList = (
[self._forcedHeaderDict["subtype url"]] if self._forcedHeaderDict["subtype url"] != "" else []
)
else:
subtypeUrlList = self.GTRACK_PRIORITIZED_SUBTYPE_LIST
for subtypeUrl in subtypeUrlList:
subtypeGESource = Gtrack.getSubtypeGESource(subtypeUrl)
subtypeColumns = subtypeGESource.getColumns(orig=False)
subtypeHeaders = subtypeGESource.getHeaderDict()
numRepeats = 2 if subtypeHeaders["subtype adherence"] == "redefinable" else 1
for repeat in range(numRepeats):
self._setHeaderDict("1-indexed", subtypeHeaders["1-indexed"])
self._setHeaderDict("end inclusive", subtypeHeaders["end inclusive"])
if subtypeHeaders["subtype adherence"] in ["reorderable", "free"]:
rearrangedColumns = columns
rearrangedHbColumns = hbColumns
else:
colSet = set(columns)
subtypeColSet = set(subtypeColumns)
if subtypeHeaders["subtype adherence"] == "redefinable":
colsRemoved = list(subtypeColSet - colSet)
colsAdded = list(colSet - subtypeColSet)
if len(colsRemoved) != len(colsAdded) or len(colsRemoved) > 2:
continue
colsRedefinedTo = ["value", "edges"] if repeat == 1 else ["edges", "value"]
rearrangedColumns = []
i, j = (0, 0)
for col in subtypeColumns:
if col in colsRemoved:
rearrangedColumns.append(colsRedefinedTo[i])
i += 1
elif col in colsRedefinedTo:
rearrangedColumns.append(colsAdded[j])
j += 1
else:
rearrangedColumns.append(col)
for col in columns:
if col in colsAdded[j:]:
rearrangedColumns.append(col)
else:
rearrangedColumns = [x for x in subtypeColumns if x in colSet] + [
x for x in columns if x not in subtypeColSet
]
rearrangedHbColumns = self._getHbColumnsFromGtrackColumns(rearrangedColumns)
try:
tempFile = StringIO()
self._composeContents(
tempFile,
rearrangedHbColumns,
rearrangedColumns,
deepcopy(self._geSource),
onlyNonDefault=True,
singleDataLine=True,
)
gtrackGESource = Gtrack(
"subtype.test." + self.getDefaultFileNameSuffix(),
printWarnings=False,
strToUseInsteadOfFn=tempFile.getvalue(),
)
tempFile.close()
if gtrackGESource.compliesWithSubtype(subtypeUrl):
gtrackGESource._headerDict["subtype url"] = subtypeUrl
gtrackGESource._updateHeadersAccordingToSubtype()
updatedHeaders = OrderedDict(
[
(key, val)
for key, val in gtrackGESource.getHeaderDict().iteritems()
if val != Gtrack.DEFAULT_HEADER_DICT.get(key)
]
)
for header in updatedHeaders:
self._setHeaderDict(header, updatedHeaders[header])
return rearrangedHbColumns, rearrangedColumns, True
except Exception, e:
continue
