def testHeaderExpansion(self):
geSourceTest = self._commonSetup()
for caseName in geSourceTest.cases:
if not caseName.startswith('gtrack'):
continue
if 'no_expand' in caseName:
print 'Test case skipped: ' + caseName
continue
onlyGuaranteed = 'no_types_expanded' in caseName
print caseName
print '==========='
case = geSourceTest.cases[caseName]
headerLines = [line if not self._isHeaderLine(line) else
'##' + ': '.join([str(x).lower() for x in Gtrack.getHeaderKeyValue(line.strip())])
for line in case.headerLines]
fullContents = os.linesep.join(headerLines + case.lines)
print 'Original:\n\n' + fullContents
case.headerLines = [line for line in headerLines if not self._isExpandableHeader(line, onlyGuaranteed)]
print '-----'
print 'With headers removed:\n\n' + os.linesep.join(case.headerLines + case.lines)
testFn = self._writeTestFile(case)
expandedContents = expandHeadersOfGtrackFileAndReturnContents(testFn, case.genome, onlyNonDefault=False)
print '-----'
print 'With expanded headers:\n\n' + expandedContents
expandedContentsOnlyNonDefaults = expandHeadersOfGtrackFileAndReturnContents(testFn, case.genome, onlyNonDefault=True)
print '-----'
print 'With expanded headers (only non-default headers):\n\n' + expandedContentsOnlyNonDefaults
origExpandableHeaders = dict([Gtrack.getHeaderKeyValue(line) for line in headerLines \
if self._isExpandableHeader(line, onlyGuaranteed=False)])
notExpandableHeaders = dict([Gtrack.getHeaderKeyValue(line) for line in case.headerLines \
if self._isHeaderLine(line) and not self._isValueNotKeptHeader(line)])
expandedHeaders = dict([Gtrack.getHeaderKeyValue(line) for line in expandedContents.split(os.linesep) \
if self._isHeaderLine(line)])
if 'no_check_expand' in caseName:
print 'No checks for case: ' + caseName
else:
for header in origExpandableHeaders:
self.assertEquals(origExpandableHeaders[header], expandedHeaders[header])
for header in notExpandableHeaders:
self.assertEquals(notExpandableHeaders[header], expandedHeaders[header])
for contents in [expandedContents, expandedContentsOnlyNonDefaults]:
sourceClass = GenomeElementSource if case.sourceClass is None else case.sourceClass
forPreProcessor = True if case.sourceClass is None else False
stdGeSource = GEDependentAttributesHolder(sourceClass('expanded.gtrack', case.genome, \
forPreProcessor=forPreProcessor, \
printWarnings=False, \
strToUseInsteadOfFn=contents))
def _isValueNotKeptHeader(self, line):
return self._isHeaderLine(line) and \
Gtrack.getHeaderKeyValue(line)[0] in VALUE_NOT_KEPT_HEADERS
def _isExpandableHeader(self, line, onlyGuaranteed):
return self._isHeaderLine(line) and \
( (Gtrack.getHeaderKeyValue(line)[0] in EXPANDABLE_HEADERS) or \
(not onlyGuaranteed and Gtrack.getHeaderKeyValue(line)[0] in NOT_GUARANTEED_EXPANDABLE_HEADERS) )
def testHeaderExpansion(self):
geSourceTest = self._commonSetup()
for caseName in geSourceTest.cases:
if not caseName.startswith('gtrack'):
continue
if 'no_expand' in caseName:
print 'Test case skipped: ' + caseName
continue
onlyGuaranteed = 'no_types_expanded' in caseName
print caseName
print '==========='
case = geSourceTest.cases[caseName]
headerLines = [line if not self._isHeaderLine(line) else
'##' + ': '.join([str(x).lower() for x in Gtrack.getHeaderKeyValue(line.strip())])
for line in case.headerLines]
fullContents = os.linesep.join(headerLines + case.lines)
print 'Original:\n\n' + fullContents
case.headerLines = [line for line in headerLines if not self._isExpandableHeader(line, onlyGuaranteed)]
print '-----'
print 'With headers removed:\n\n' + os.linesep.join(case.headerLines + case.lines)
testFn = self._writeTestFile(case)
expandedContents = expandHeadersOfGtrackFileAndReturnContents(testFn, case.genome, onlyNonDefault=False)
print '-----'
print 'With expanded headers:\n\n' + expandedContents
expandedContentsOnlyNonDefaults = expandHeadersOfGtrackFileAndReturnContents(testFn, case.genome, onlyNonDefault=True)
print '-----'
print 'With expanded headers (only non-default headers):\n\n' + expandedContentsOnlyNonDefaults
origExpandableHeaders = dict([Gtrack.getHeaderKeyValue(line) for line in headerLines \
if self._isExpandableHeader(line, onlyGuaranteed=False)])
notExpandableHeaders = dict([Gtrack.getHeaderKeyValue(line) for line in case.headerLines \
if self._isHeaderLine(line) and not self._isValueNotKeptHeader(line)])
expandedHeaders = dict([Gtrack.getHeaderKeyValue(line) for line in expandedContents.split(os.linesep) \
if self._isHeaderLine(line)])
if 'no_check_expand' in caseName:
print 'No checks for case: ' + caseName
else:
for header in origExpandableHeaders:
self.assertEquals(origExpandableHeaders[header], expandedHeaders[header])
for header in notExpandableHeaders:
self.assertEquals(notExpandableHeaders[header], expandedHeaders[header])
for contents in [expandedContents, expandedContentsOnlyNonDefaults]:
sourceClass = GenomeElementSource if case.sourceClass is None else case.sourceClass
forPreProcessor = True if case.sourceClass is None else False
stdGeSource = GEDependentAttributesHolder(sourceClass('expanded.gtrack', case.genome, \
forPreProcessor=forPreProcessor, \
printWarnings=False, \
strToUseInsteadOfFn=contents))
self.assertEquals(case.assertElementList, [ge for ge in stdGeSource])
self.assertEquals(case.boundingRegionsAssertList, [br for br in stdGeSource.getBoundingRegionTuples()])
def _isValueNotKeptHeader(self, line):
return self._isHeaderLine(line) and \
Gtrack.getHeaderKeyValue(line)[0] in VALUE_NOT_KEPT_HEADERS
def _isExpandableHeader(self, line, onlyGuaranteed):
return self._isHeaderLine(line) and \
( (Gtrack.getHeaderKeyValue(line)[0] in EXPANDABLE_HEADERS) or \
(not onlyGuaranteed and Gtrack.getHeaderKeyValue(line)[0] in NOT_GUARANTEED_EXPANDABLE_HEADERS) )