def __init__( self, input_gtf_false_path, data_gtf):
super(Gtf, self).__init__()
self.track = None
self.input_gtf_false_path = input_gtf_false_path
self.name_gtf = data_gtf["name"]
self.priority = data_gtf["order_index"]
#print "Creating TrackHub GTF from (falsePath: %s; name: %s)" % ( self.input_gtf_false_path, self.name_gtf)
# TODO: See if we need these temporary files as part of the generated files
genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed")
sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
# GtfToGenePred
subtools.gtfToGenePred(self.input_gtf_false_path, genePredFile.name)
# TODO: From there, refactor because common use with Gff3.py
# genePredToBed processing
subtools.genePredToBed(genePredFile.name, unsortedBedFile.name)
# Sort processing
subtools.sort(unsortedBedFile.name, sortedBedFile.name)
# bedToBigBed processing
# TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
trackName = "".join( ( self.name_gtf, ".bb") )
myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
with open(myBigBedFilePath, 'w') as bigBedFile:
subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)
# Create the Track Object
self.createTrack(file_path=trackName,
track_name=trackName,
long_label=self.name_gtf, track_type='bigBed 12 +', visibility='dense', priority=self.priority,
track_file=myBigBedFilePath)
#
# dataURL = "tracks/%s" % trackName
#
# trackDb = TrackDb(
# trackName=trackName,
# longLabel=self.name_gtf,
# shortLabel=self.getShortName( self.name_gtf ),
# trackDataURL=dataURL,
# trackType='bigBed 12 +',
# visibility='dense',
# priority=self.priority,
# )
# self.track = Track(
# trackFile=myBigBedFilePath,
# trackDb=trackDb,
# )
print("- Gtf %s created" % self.name_gtf)
def __init__( self, inputBedGeneric, data_bed_generic):
super(Bed, self).__init__()
self.track = None
self.inputBedGeneric = inputBedGeneric
self.sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
self.data_bed_generic = data_bed_generic
self.name_bed_generic = self.data_bed_generic["name"]
self.priority = self.data_bed_generic["order_index"]
# Sort processing
subtools.sort(self.inputBedGeneric, self.sortedBedFile.name)
# bedToBigBed processing
# TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
trackName = "".join( ( self.name_bed_generic, ".bb") )
myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
with open(myBigBedFilePath, 'w') as self.bigBedFile:
subtools.bedToBigBed(self.sortedBedFile.name, self.chromSizesFile.name, self.bigBedFile.name)
# Create the Track Object
self.createTrack(file_path=trackName,
track_name=trackName,
long_label=self.name_bed_generic, track_type='bigBed', visibility='dense',
priority=self.priority,
track_file=myBigBedFilePath)
# dataURL = "tracks/%s" % trackName
#
# trackDb = TrackDb(
# trackName=trackName,
# longLabel=self.name_bed_generic,
# shortLabel=self.getShortName(self.name_bed_generic),
# trackDataURL=dataURL,
# trackType='bigBed',
# visibility='dense',
# thickDrawItem='on',
# priority=self.priority,
# )
#
# # Return the BigBed track
# self.track = Track(
# trackFile=myBigBedFilePath,
# trackDb=trackDb,
# )
print("- Bed %s created" % self.name_bed_generic)
def __init__(self, input_bed_simple_repeats_false_path, data_bed_simple_repeats):
super(BedSimpleRepeats, self).__init__()
self.input_bed_simple_repeats_false_path = input_bed_simple_repeats_false_path
self.name_bed_simple_repeats = data_bed_simple_repeats["name"]
self.priority = data_bed_simple_repeats["order_index"]
sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
# Sort processing
subtools.sort(self.input_bed_simple_repeats_false_path, sortedBedFile.name)
# bedToBigBed processing
# TODO: Change the name of the bb, to tool + genome + .bb
trackName = "".join( ( self.name_bed_simple_repeats, '.bb' ) )
myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
auto_sql_option = "%s%s" % ('-as=', os.path.join(self.tool_directory, 'trf_simpleRepeat.as'))
with open(myBigBedFilePath, 'w') as bigBedFile:
subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name,
typeOption='-type=bed4+12',
autoSql=auto_sql_option)
# Create the Track Object
self.createTrack(file_path=trackName,
track_name=trackName,
long_label=self.name_bed_simple_repeats, track_type='bigBed 4 +', visibility='dense',
priority=self.priority,
track_file=myBigBedFilePath)
# dataURL = "tracks/%s" % trackName
#
# trackDb = TrackDb(
# trackName=trackName,
# longLabel=self.name_bed_simple_repeats,
# shortLabel=self.getShortName( self.name_bed_simple_repeats ),
# trackDataURL=dataURL,
# trackType='bigBed 4 +',
# visibility='dense',
# priority=self.priority,
# )
#
# self.track = Track(
# trackFile=myBigBedFilePath,
# trackDb=trackDb,
# )
print("- Bed simple repeats %s created" % self.name_bed_simple_repeats)
def __init__(self, input_Gff3_false_path, data_gff3):
super(Gff3, self).__init__()
self.track = None
self.input_Gff3_false_path = input_Gff3_false_path
self.name_gff3 = data_gff3["name"]
self.priority = data_gff3["order_index"]
# TODO: See if we need these temporary files as part of the generated files
genePredFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".genePred")
unsortedBedFile = tempfile.NamedTemporaryFile(bufsize=0, suffix=".unsortedBed")
sortedBedFile = tempfile.NamedTemporaryFile(suffix=".sortedBed")
# TODO: Refactor into another Class to manage the twoBitInfo and ChromSizes (same process as in Gtf.py)
# gff3ToGenePred processing
subtools.gff3ToGenePred(self.input_Gff3_false_path, genePredFile.name)
# TODO: From there, refactor because common use with Gtf.py
# genePredToBed processing
subtools.genePredToBed(genePredFile.name, unsortedBedFile.name)
# Sort processing
subtools.sort(unsortedBedFile.name, sortedBedFile.name)
# TODO: Check if no errors
# bedToBigBed processing
# TODO: Change the name of the bb, to tool + genome + possible adding if multiple + .bb
trackName = "".join((self.name_gff3, ".bb"))
myBigBedFilePath = os.path.join(self.myTrackFolderPath, trackName)
with open(myBigBedFilePath, "w") as bigBedFile:
subtools.bedToBigBed(sortedBedFile.name, self.chromSizesFile.name, bigBedFile.name)
# Create the Track Object
self.createTrack(
file_path=trackName,
track_name=trackName,
long_label=self.name_gff3,
track_type="bigBed 12 +",
visibility="dense",
priority=self.priority,
track_file=myBigBedFilePath,
)
# dataURL = "tracks/%s" % trackName
#
# trackDb = TrackDb(
# trackName=trackName,
# longLabel=self.name_gff3,
# shortLabel=self.getShortName( self.name_gff3 ),
# trackDataURL=dataURL,
# trackType='bigBed 12 +',
# visibility='dense',
# priority=self.priority,
# )
#
# self.track = Track(
# trackFile=myBigBedFilePath,
# trackDb=trackDb,
# )
print("- Gff3 %s created" % self.name_gff3)