def getTrackExtractionOptions(genome, trackName):
from gtrackcore.track.core.Track import PlainTrack
from gtrackcore.input.userbins.UserBinSource import MinimalBinSource
from gtrackcore.extract.fileformats.FileFormatComposer import \
findMatchingFileFormatComposers, getComposerClsFromFileSuffix
tf = PlainTrack(trackName).getTrackView(
MinimalBinSource(genome)[0]).trackFormat
extractionOptions = []
matchingComposers = findMatchingFileFormatComposers(tf)
for composerInfo in matchingComposers:
allOverlapRules = tf.getAllOverlapRules()
for allowOverlaps in allOverlapRules:
extractionOptions.append( \
(composerInfo.trackFormatName.capitalize() + \
' ' + TrackExtractor.getFileFormatText(composerInfo.fileFormatName) + \
(', ' + (TrackExtractor.ALLOW_OVERLAPS_TRUE_TEXT if allowOverlaps else \
TrackExtractor.ALLOW_OVERLAPS_FALSE_TEXT) \
if len(allOverlapRules) > 1 else ''), \
composerInfo.fileSuffix) )
ti = TrackInfo(genome, trackName)
if ti.fileType != '':
try:
extractionOptions.append(
(TrackExtractor.ORIG_FILE_FORMAT_TEXT.capitalize() + \
' ' + TrackExtractor.getFileSuffixText(ti.fileType), \
getComposerClsFromFileSuffix(ti.fileType).getDefaultFileNameSuffix()))
except Exception, e:
print 'Error:', e
def getTrackExtractionOptions(genome, trackName):
from gtrackcore.track.core.Track import PlainTrack
from gtrackcore.input.userbins.UserBinSource import MinimalBinSource
from gtrackcore.extract.fileformats.FileFormatComposer import \
findMatchingFileFormatComposers, getComposerClsFromFileSuffix
tf = PlainTrack(trackName).getTrackView(MinimalBinSource(genome)[0]).trackFormat
extractionOptions = []
matchingComposers = findMatchingFileFormatComposers(tf)
for composerInfo in matchingComposers:
allOverlapRules = tf.getAllOverlapRules()
for allowOverlaps in allOverlapRules:
extractionOptions.append( \
(composerInfo.trackFormatName.capitalize() + \
' ' + TrackExtractor.getFileFormatText(composerInfo.fileFormatName) + \
(', ' + (TrackExtractor.ALLOW_OVERLAPS_TRUE_TEXT if allowOverlaps else \
TrackExtractor.ALLOW_OVERLAPS_FALSE_TEXT) \
if len(allOverlapRules) > 1 else ''), \
composerInfo.fileSuffix) )
ti = TrackInfo(genome, trackName)
if ti.fileType != '':
try:
extractionOptions.append(
(TrackExtractor.ORIG_FILE_FORMAT_TEXT.capitalize() + \
' ' + TrackExtractor.getFileSuffixText(ti.fileType), \
getComposerClsFromFileSuffix(ti.fileType).getDefaultFileNameSuffix()))
except Exception, e:
print 'Error:', e
