def isValidTrack(genome, trackName, fullAccess=False):
if not TrackInfo(genome, trackName).isValid(fullAccess):
return False
for fn in ProcTrackOptions._getDirContents(genome, trackName):
if GenomeInfo.isValidChr(genome, fn) or isBoundingRegionFileName(fn):
return True
return False
def _checkValidStart(self, chr, start):
if start < 0:
raise InvalidFormatError('Error: start position is negative: %s' % start)
if self.genome and \
GenomeInfo.isValidChr(self.genome, chr) and \
start > GenomeInfo.getChrLen(self.genome, chr):
raise InvalidFormatError('Error: start position is larger than the size of chromosome "%s" (%s > %s)' % \
(chr, start, GenomeInfo.getChrLen(self.genome, chr)))
return start
def getSubtypes(genome, trackName, fullAccess=False):
dirPath = createDirPath(trackName, genome)
subtypes = [fn for fn in ProcTrackOptions._getDirContents(genome, trackName) \
if not (fn[0] in ['.','_'] or os.path.isfile(dirPath + os.sep + fn) \
or GenomeInfo.isValidChr(genome, fn))]
#fixme, just temporarily:, these dirs should start with _
subtypes= [x for x in subtypes if not x in ['external','ucsc'] ]
#if not fullAccess and not ProcTrackOptions._isLiteratureTrack(genome, trackName):
# subtypes = [x for x in subtypes if not TrackInfo(genome, trackName+[x]).private]
return sorted(subtypes, key=str.lower)
def _checkValidEnd(self, chr, end, start=None):
if end < 0:
raise InvalidFormatError('Error: end position is negative: %s' % end)
if self.genome and \
GenomeInfo.isValidChr(self.genome, chr) and \
end-1 > GenomeInfo.getChrLen(self.genome, chr):
raise InvalidFormatError('Error: end position is larger than the size of chromosome "%s" (%s > %s)' % \
(chr, end-1, GenomeInfo.getChrLen(self.genome, chr)))
if start is not None and end <= start:
if not start == end == 1:
raise InvalidFormatError('Error: end position (end-exclusive) is smaller than or equal to start position: %d <= %d' % (end, start))
return end
def _checkValidChr(self, chr):
if self.genome and not GenomeInfo.isValidChr(self.genome, chr):
raise InvalidFormatWarning('Chromosome incorrectly specified: ' + chr)
return chr
