def _add_tracks(data_list, view, default_tracktype):
for data_obj in data_list:
kwargs = data_obj.obj.get('trackinfo', {})
kwargs = dict((k, str(v)) for k, v in kwargs.items())
kwargs.setdefault('tracktype', default_tracktype)
view.add_tracks(
Track(
name=sanitized_label + utils.sanitize(data_obj.label),
short_label=data_obj.label,
long_label=data_obj.obj['long_label'],
local_fn=data_obj.processed,
**kwargs))
def _add_tracks(data_list, view, default_tracktype):
for data_obj in data_list:
kwargs = data_obj.obj.get('trackinfo', {})
kwargs = dict((k, str(v)) for k, v in kwargs.items())
kwargs.setdefault('tracktype', default_tracktype)
view.add_tracks(
Track(name=sanitized_label +
utils.sanitize(data_obj.label),
short_label=data_obj.label,
long_label=data_obj.obj['long_label'],
local_fn=data_obj.processed,
**kwargs))
def composite_track(self):
"""
Create a composite track ready to be added to a trackhub.TrackDb
instance.
"""
bigwigs = [i for i in self.tracks if i.type_ == 'bigwig']
bigbeds = [i for i in self.tracks if i.type_ == 'bigbed']
bams = [i for i in self.tracks if i.type_ == 'bam']
# Build the HTML docs
last_section = self.reference_section()
html_string = utils.reST_to_html(
self.metadata['study'].get('description', '') + '\n' + last_section)
sanitized_label = utils.sanitize(self.label, strict=True)
# Composite track to hold all subtracks for the study
composite = CompositeTrack(
name=sanitized_label,
short_label=self.study['short_label'],
long_label=self.study['long_label'],
tracktype='bigBed',
# Add all the documentation
html_string=html_string)
# If there are any bigWigs defined for this study, make a new "signal"
# subtrack in the composite and then add the bigWigs to it.
#
# Uses the sanitized label for the study to ensure uniqueness among
# tracks.
#
def _add_tracks(data_list, view, default_tracktype):
for data_obj in data_list:
kwargs = data_obj.obj.get('trackinfo', {})
kwargs = dict((k, str(v)) for k, v in kwargs.items())
kwargs.setdefault('tracktype', default_tracktype)
view.add_tracks(
Track(
name=sanitized_label + utils.sanitize(data_obj.label),
short_label=data_obj.label,
long_label=data_obj.obj['long_label'],
local_fn=data_obj.processed,
**kwargs))
if len(bigwigs) > 0:
signal_view = ViewTrack(
name=sanitized_label + 'signalviewtrack',
view=sanitized_label + 'signalview',
short_label=self.label + ' signal view',
long_label=self.label + ' signal view',
visibility='full',
maxHeightPixels='100:25:8',
autoScale='off',
tracktype='bigWig',
)
composite.add_view(signal_view)
_add_tracks(bigwigs, signal_view, 'bigWig')
# Same thing with bigBeds
if len(bigbeds) > 0:
bed_view = ViewTrack(
name=sanitized_label + 'bedviewtrack',
view=sanitized_label + 'bed_view',
short_label=self.label + ' bed view',
long_label=self.label + ' bed view',
visibility='dense',
)
composite.add_view(bed_view)
_add_tracks(bigbeds, bed_view, 'bigBed 9')
# and bams
if len(bams) > 0:
bam_view = ViewTrack(
name=sanitized_label + 'bamviewtrack',
view=sanitized_label + 'bam_view',
short_label=self.label + ' bam view',
long_label=self.label + ' bam view',
visibility='dense',
)
composite.add_view(bam_view)
_add_tracks(bams, bam_view, 'bam')
return composite
def composite_track(self):
"""
Create a composite track ready to be added to a trackhub.TrackDb
instance.
"""
bigwigs = [i for i in self.tracks if i.type_ == 'bigwig']
bigbeds = [i for i in self.tracks if i.type_ == 'bigbed']
# Build the HTML docs
last_section = self.reference_section()
html_string = utils.reST_to_html(
self.metadata['study'].get('description', '') + '\n' +
last_section)
sanitized_label = utils.sanitize(self.label, strict=True)
# Composite track to hold all subtracks for the study
composite = CompositeTrack(
name=sanitized_label,
short_label=self.study['short_label'],
long_label=self.study['long_label'],
tracktype='bigBed',
# Add all the documentation
html_string=html_string)
# If there are any bigWigs defined for this study, make a new "signal"
# subtrack in the composite and then add the bigWigs to it.
#
# Uses the sanitized label for the study to ensure uniqueness among
# tracks.
#
def _add_tracks(data_list, view, default_tracktype):
for data_obj in data_list:
kwargs = data_obj.obj.get('trackinfo', {})
kwargs = dict((k, str(v)) for k, v in kwargs.items())
kwargs.setdefault('tracktype', default_tracktype)
view.add_tracks(
Track(name=sanitized_label +
utils.sanitize(data_obj.label),
short_label=data_obj.label,
long_label=data_obj.obj['long_label'],
local_fn=data_obj.processed,
**kwargs))
if len(bigwigs) > 0:
signal_view = ViewTrack(
name=sanitized_label + 'signalviewtrack',
view=sanitized_label + 'signalview',
short_label=self.label + ' signal view',
long_label=self.label + ' signal view',
visibility='full',
maxHeightPixels='100:25:8',
autoScale='off',
tracktype='bigWig',
)
composite.add_view(signal_view)
_add_tracks(bigwigs, signal_view, 'bigWig')
# Same thing with bigBeds
if len(bigbeds) > 0:
bed_view = ViewTrack(
name=sanitized_label + 'bedviewtrack',
view=sanitized_label + 'bed_view',
short_label=self.label + ' bed view',
long_label=self.label + ' bed view',
visibility='dense',
)
composite.add_view(bed_view)
_add_tracks(bigbeds, bed_view, 'bigBed 9')
return composite