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
def getAttrsFromExtractionFormat(cls, extractionFormat):
asOriginal = extractionFormat.lower().startswith(cls.ORIG_FILE_FORMAT_TEXT)
if asOriginal:
suffix = TrackExtractor.getFileSuffixFromExtractionFormat(extractionFormat)
from gtrackcore.extract.fileformats.FileFormatComposer import getComposerClsFromFileSuffix
composerCls = getComposerClsFromFileSuffix(suffix)
fileFormatName = composerCls.FILE_FORMAT_NAME
allowOverlaps = True
else:
fileFormatName = cls.getFileFormatNameFromExtractionFormat(extractionFormat)
allowOverlaps = extractionFormat.lower().endswith(cls.ALLOW_OVERLAPS_TRUE_TEXT)
return fileFormatName, asOriginal, allowOverlaps
def getAttrsFromExtractionFormat(cls, extractionFormat):
asOriginal = extractionFormat.lower().startswith(
cls.ORIG_FILE_FORMAT_TEXT)
if asOriginal:
suffix = TrackExtractor.getFileSuffixFromExtractionFormat(
extractionFormat)
from gtrackcore.extract.fileformats.FileFormatComposer import getComposerClsFromFileSuffix
composerCls = getComposerClsFromFileSuffix(suffix)
fileFormatName = composerCls.FILE_FORMAT_NAME
allowOverlaps = True
else:
fileFormatName = cls.getFileFormatNameFromExtractionFormat(
extractionFormat)
allowOverlaps = extractionFormat.lower().endswith(
cls.ALLOW_OVERLAPS_TRUE_TEXT)
return fileFormatName, asOriginal, allowOverlaps
def extract(cls, trackName, regionList, fn, fileFormatName=DEFAULT_FILE_FORMAT_NAME, globalCoords=True, \
addSuffix=False, asOriginal=False, allowOverlaps=False, ignoreEmpty=False):
from gtrackcore.input.adapters.TrackGenomeElementSource import TrackGenomeElementSource
from gtrackcore.extract.fileformats.FileFormatComposer import getComposerClsFromFileFormatName, getComposerClsFromFileSuffix
assert len(regionList) > 0
for region in regionList:
genome = region.genome
break
#To silently extract correctly if track type is dense
if allowOverlaps:
allowOverlaps = os.path.exists(
createDirPath(trackName, genome, allowOverlaps=True))
trackGESource = TrackGenomeElementSource(genome, trackName, regionList, globalCoords=globalCoords, \
allowOverlaps=allowOverlaps, printWarnings=False)
composerCls = None
if asOriginal:
ti = TrackInfo(genome, trackName)
if ti.fileType != '':
try:
composerCls = getComposerClsFromFileSuffix(ti.fileType)
except:
pass
if composerCls is None:
composerCls = getComposerClsFromFileFormatName(fileFormatName)
if addSuffix:
fn = os.path.splitext(
fn)[0] + '.' + composerCls.getDefaultFileNameSuffix()
composer = composerCls(trackGESource)
ok = composer.composeToFile(fn, ignoreEmpty=ignoreEmpty)
if ok:
return fn
def extract(cls, trackName, regionList, fn, fileFormatName=DEFAULT_FILE_FORMAT_NAME, globalCoords=True, \
addSuffix=False, asOriginal=False, allowOverlaps=False, ignoreEmpty=False):
from gtrackcore.input.adapters.TrackGenomeElementSource import TrackGenomeElementSource
from gtrackcore.extract.fileformats.FileFormatComposer import getComposerClsFromFileFormatName, getComposerClsFromFileSuffix
assert len(regionList) > 0
for region in regionList:
genome = region.genome
break
#To silently extract correctly if track type is dense
if allowOverlaps:
allowOverlaps = os.path.exists(createDirPath(trackName, genome, allowOverlaps=True))
trackGESource = TrackGenomeElementSource(genome, trackName, regionList, globalCoords=globalCoords, \
allowOverlaps=allowOverlaps, printWarnings=False)
composerCls = None
if asOriginal:
ti = TrackInfo(genome, trackName)
if ti.fileType != '':
try:
composerCls = getComposerClsFromFileSuffix(ti.fileType)
except:
pass
if composerCls is None:
composerCls = getComposerClsFromFileFormatName(fileFormatName)
if addSuffix:
fn = os.path.splitext(fn)[0] + '.' + composerCls.getDefaultFileNameSuffix()
composer = composerCls(trackGESource)
ok = composer.composeToFile(fn, ignoreEmpty=ignoreEmpty)
if ok:
return fn