def getOptionsBox6(prevChoices):
if prevChoices[3]:
extraDbColumnsDict = OrderedDict()
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(prevChoices[2].split(':'))
fnDB = ExternalTrackManager.extractFnFromGalaxyTN(prevChoices[3].split(':'))
gtrackDB = GtrackGenomeElementSource(fnDB)
gtrackSource = GtrackGenomeElementSource(fnSource)
extraDbColumns = [v for v in gtrackDB.getColumns() if not v in gtrackSource.getColumns()] #list(set(gtrackDBColumnSpec) - set(gtrackSourceColumnSpec))
for column in extraDbColumns:
extraDbColumnsDict[column] = False
return extraDbColumnsDict
def _getHeaders(prevChoices):
numCols = TabularToGtrackTool._getFileContentsInfo(prevChoices).numCols
if prevChoices.columnSelection != 'Base columns on existing GTrack file':
header = []
for i in xrange(numCols):
if hasattr(prevChoices, 'column%s' % i):
colHeader = getattr(prevChoices, 'column%s' % i)
if colHeader is None or colHeader == '-- ignore --':
header.append('')
elif colHeader == '-- custom --':
header.append(getattr(prevChoices, 'customColumn%s' % i).strip())
else:
header.append(colHeader)
else:
header.append('')
return header
else:
genome = prevChoices.genome if prevChoices.selectGenome == 'Yes' else None
try:
inFn = ExternalTrackManager.extractFnFromGalaxyTN(prevChoices.colSpecFile.split(':'))
geSource = GtrackGenomeElementSource(inFn, genome=genome)
geSource.parseFirstDataLine()
return geSource.getColumns()[:numCols]
except Exception, e:
return []
def _getHeaders(prevChoices):
numCols = TabularToGtrackTool._getFileContentsInfo(prevChoices).numCols
if prevChoices.columnSelection == 'Select individual columns':
header = []
for i in xrange(numCols):
if hasattr(prevChoices, 'column%s' % i):
colHeader = getattr(prevChoices, 'column%s' % i)
if colHeader is None or colHeader == '-- ignore --':
header.append('')
elif colHeader == '-- custom --':
header.append(getattr(prevChoices, 'customColumn%s' % i).strip())
else:
header.append(colHeader)
else:
header.append('')
return header
else:
genome = prevChoices.genome if prevChoices.selectGenome == 'Yes' else None
inFn = ExternalTrackManager.extractFnFromGalaxyTN(prevChoices.colSpecFile.split(':'))
try:
geSource = GtrackGenomeElementSource(inFn, genome=genome)
geSource.parseFirstDataLine()
return geSource.getColumns()[:numCols]
except Exception, e:
return []
def getOptionsBox6(prevChoices):
if prevChoices[3]:
extraDbColumnsDict = OrderedDict()
fnSource = ExternalTrackManager.extractFnFromGalaxyTN(
prevChoices[2].split(':'))
fnDB = ExternalTrackManager.extractFnFromGalaxyTN(
prevChoices[3].split(':'))
gtrackDB = GtrackGenomeElementSource(fnDB)
gtrackSource = GtrackGenomeElementSource(fnSource)
extraDbColumns = [
v for v in gtrackDB.getColumns()
if not v in gtrackSource.getColumns()
] #list(set(gtrackDBColumnSpec) - set(gtrackSourceColumnSpec))
for column in extraDbColumns:
extraDbColumnsDict[column] = False
return extraDbColumnsDict