class WigTrack(Track):
"""
WigTrack as described at:
https://github.com/igvteam/igv.js/wiki/Wig-Track
"""
type = Unicode('wig', read_only=True).tag(sync=True)
autoscale = Bool(True).tag(sync=True)
autoscaleGroup = Unicode(allow_none=True).tag(sync=True, **widget_serialization_no_none)
min = Int(0).tag(sync=True)
max = Int(allow_none=True).tag(sync=True, **widget_serialization_no_none)
color = Color(default_value="rgb(150, 150, 150)").tag(sync=True)
altColor = Color(allow_none=True).tag(sync=True, **widget_serialization_no_none)
guideLines = List(trait=Instance(Guideline), allow_none=True).tag(sync=True, **widget_serialization_no_none)
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
class VariantTrack(Track):
"""
VariantTrack as described at:
https://github.com/igvteam/igv.js/wiki/Variant-Track
"""
type = Unicode('variant', read_only=True).tag(sync=True)
displayMode = Unicode('EXPANDED').tag(sync=True)
noCallColor = Color("rgb(250, 250, 250)").tag(sync=True)
homvarColor = Color("rgb(17,248,254)").tag(sync=True)
hetvarColor = Color("rgb(34,12,253)").tag(sync=True)
homrefColor = Color("rgb(200, 200, 200)").tag(sync=True)
squishedCallHeight = Int(1).tag(sync=True)
expandedCallHeight = Int(10).tag(sync=True)
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
class AlignmentTrack(Track):
"""
AlignmentTrack as described at:
https://github.com/igvteam/igv.js/wiki/Alignment-Track
"""
type = Unicode('alignment', read_only=True).tag(sync=True)
viewAsPairs = Bool(default_value=False).tag(sync=True)
pairsSupported = Bool(default_value=True).tag(sync=True)
coverageColor = Color(default_value="rgb(150, 150, 150)").tag(sync=True, **widget_serialization) # default: rgb(150, 150, 150)
color = Color(default_value="rgb(170, 170, 170)").tag(sync=True, **widget_serialization) # default: rgb(170, 170, 170)
deletionColor = Color(default_value="black").tag(sync=True, **widget_serialization)
skippedColor = Color(default_value="rgb(150, 170, 170)").tag(sync=True, **widget_serialization) # default: rgb(150, 170, 170)
insertionColor = Color(default_value="rgb(138, 94, 161)").tag(sync=True, **widget_serialization) # default: rgb(138, 94, 161)
negStrandColor = Color(default_value="rgba(150, 150, 230, 0.75)").tag(sync=True, **widget_serialization) # default: rgba(150, 150, 230, 0.75)
posStrandColor = Color(default_value="rgba(230, 150, 150, 0.75)").tag(sync=True, **widget_serialization) # default: rgb(138, 94, 161)
# pairConnectorColor = Instance(Color, default_value="alignmentColor") # default: doc not clear
colorBy = Unicode("none").tag(sync=True) # "none", "strand", "firstOfPairStrand", or "tag"
colorByTag = Unicode().tag(sync=True) # TODO - doc not clear
bamColorTag = Unicode("YC").tag(sync=True) # TODO - doc not clear
samplingWindowSize = Int(100).tag(sync=True)
samplingDepth = Int(100).tag(sync=True)
alignmentRowHeight = Int(14).tag(sync=True)
readgroup = Unicode("RG").tag(sync=True)
sortOption = Instance(SortOption, allow_none=True).tag(sync=True, **widget_serialization_no_none)
showSoftClips = Bool(False).tag(sync=True)
showMismatches = Bool(True).tag(sync=True)
# Paired-end and mate-pair coloring options.
pairOrientation = Unicode(allow_none=True).tag(sync=True, **widget_serialization_no_none) # ff, fr, or rf
minFragmentLength = Int(allow_none=True).tag(sync=True, **widget_serialization_no_none)
maxFragmentLength = Int(allow_none=True).tag(sync=True, **widget_serialization_no_none)
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
class AnnotationTrack(Track):
"""
AnnotationTrack as described at:
https://github.com/igvteam/igv.js/wiki/Annotation-Track
"""
type = Unicode('annotation', read_only=True).tag(sync=True)
displayMode = Unicode(default_value = 'COLLAPSED').tag(sync=True)
expandedRowHeight = Int (default_value = 30).tag(sync=True)
squishedRowHeight = Int (default_value = 15).tag(sync=True)
nameField = Unicode(default_value = 'Name').tag(sync=True)
maxRows = Int (default_value = 500).tag(sync=True)
searchable = Bool(default_value=False).tag(sync=True)
filterTypes = List(Unicode, default_value=['chromosone', 'gene']).tag(sync=True, **widget_serialization_no_none)
color = Color("rgb(0,0,150)").tag(sync=True)
altColor = Color("rgb(0,0,150)").tag(sync=True)
colorBy = Instance(FieldColors, allow_none=True).tag(sync=True, **widget_serialization_no_none)
roi = List(InstanceDict(Track)).tag(sync=True, **widget_serialization_no_none) # regions of interest
class Track(Widget):
"""
A class reflecting the common fields of a track as per igv documentation.
https://github.com/igvteam/igv.js/wiki/Tracks-2.0
If a Track type is not inferable a generic Track will be instantiated.
"""
# Name of the widget view class in front-end
_view_name = Unicode('TrackView').tag(sync=True)
# Name of the widget model class in front-end
_model_name = Unicode('TrackModel').tag(sync=True)
# Name of the front-end module containing widget view
_view_module = Unicode('jupyter-igv').tag(sync=True)
# Name of the front-end module containing widget model
_model_module = Unicode('jupyter-igv').tag(sync=True)
# Version of the front-end module containing widget view
_view_module_version = Unicode(EXTENSION_VERSION).tag(sync=True)
# Version of the front-end module containing widget model
_model_module_version = Unicode(EXTENSION_VERSION).tag(sync=True)
def __new__(cls, **kwargs):
if cls is Track:
# we must infer the type to instantiate the right Track type
trackType = kwargs.get('type', None)
if trackType is None:
# then type is inferred from the file extension
url = kwargs.get('url')
path = urlparse(url).path
filename, filetype = os.path.splitext(path)
if filetype == '.gz': # some files might be compressed
innerfilename, innerfiletype = os.path.splitext(filename)
filetype = innerfiletype
for k, v in TRACK_FILE_TYPES.items():
if filetype in v:
trackType = k
break
if trackType == 'annotation':
return super(Track, cls).__new__(AnnotationTrack)
elif trackType == 'alignment':
return super(Track, cls).__new__(AlignmentTrack)
elif trackType == 'variant':
return super(Track, cls).__new__(VariantTrack)
elif trackType == 'wig':
return super(Track, cls).__new__(WigTrack)
elif trackType == 'seg':
return super(Track, cls).__new__(SegTrack)
elif trackType == 'spliceJunctions':
return super(Track, cls).__new__(SpliceJunctionsTrack)
elif trackType == 'gwas':
return super(Track, cls).__new__(GwassTrack)
elif trackType == 'interation':
return super(Track, cls).__new__(InteractionTrack)
else:
return super(Track, cls).__new__(cls)
else:
return super(Track, cls).__new__(cls)
# These fields are common to all Track types
sourceType = Unicode(default_value='file').tag(sync=True) #
format = Unicode().tag(sync=True) # missing documentation
name = Unicode().tag(sync=True)
url = Unicode().tag(sync=True)
indexURL = Unicode().tag(sync=True)
indexed = Bool(default_value=False).tag(sync=True)
order = Int().tag(sync=True)
color = Color().tag(sync=True).tag(sync=True)
height = Int(default_value=50).tag(sync=True)
autoHeight = Bool(default_value=False).tag(sync=True)
minHeight = Int(default_value=50).tag(sync=True)
maxHeight = Int(default_value=500).tag(sync=True)
# visibilityWindow = # missing documentation
removable = Bool(default_value=True).tag(sync=True)
headers = Dict().tag(sync=True)
oauthToken = Unicode(allow_none = True).tag(sync=True)
class Guideline(HasTraits):
color = Color().tag(sync=True)
dotted = Bool().tag(sync=True)
y = Int().tag(sync=True)