def __init__(self,
genome,
twobit_file=None,
remote_fn=None,
groups=None,
trackdb=None,
genome_file_obj=None,
html_string=None,
**kwargs):
"""
Represents a genome stanza within a "genomes.txt" file for a non-UCSC genome.
The file itself is represented by a :class:`GenomesFile` object.
"""
HubComponent.__init__(self)
Genome.__init__(self, genome, trackdb=trackdb, genome_file_obj=genome_file_obj)
self.local_fn = twobit_file
self.remote_fn = remote_fn
self.html_string = html_string
if groups is not None:
self.add_groups(groups)
else:
self.groups = None
self._orig_kwargs = kwargs
self.add_params(**kwargs)
def __init__(self,
genome,
twobit_file=None,
remote_fn=None,
groups=None,
trackdb=None,
genome_file_obj=None,
html_string=None,
**kwargs):
"""
Represents a genome stanza within a "genomes.txt" file for a non-UCSC genome.
The file itself is represented by a :class:`GenomesFile` object.
"""
HubComponent.__init__(self)
Genome.__init__(self,
genome,
trackdb=trackdb,
genome_file_obj=genome_file_obj)
self.local_fn = twobit_file
self.remote_fn = remote_fn
self.html_string = html_string
if groups is not None:
self.add_groups(groups)
else:
self.groups = None
self._orig_kwargs = kwargs
self.add_params(**kwargs)
def __init__(self, name, tracktype=None, short_label=None,
long_label=None, subgroups=None, local_fn=None,
remote_fn=None, html_string=None, **kwargs):
"""
Represents a single track stanza.
:param name: String; name of the track
:param tracktype: String; type of the track (e.g., "bam")
:param url: String; full URL for the track (i.e., bigDataUrl)
:param short_label: String; used for the left-hand side track label
:param long_label:
String; used for the longer middle labels; if None will copy
short_label
:param subgroups:
A dictionary of `{name: tag}` where each `name` is the name of
a SubGroupDefinition in a parent :class:`CompositeTrack` and each
`tag` is a key in the SubGroupDefinition.mapping dictionary. They
end up looking like this in the string representation::
subGroups view=aln celltype=ES
:param local_fn:
String; Local path to the file (used for uploading)
:param remote_fn:
String; path to upload the file to, over rsync and ssh.
"""
HubComponent.__init__(self)
_check_name(name)
self.name = name
self.tracktype = tracktype
if short_label is None:
short_label = name
self.short_label = short_label
if long_label is None:
long_label = short_label
self.long_label = long_label
self._local_fn = local_fn
self._remote_fn = remote_fn
self.html_string = html_string
self.subgroups = {}
self.add_subgroups(subgroups)
# Convert pythonic strings to UCSC versions
kwargs['track'] = name
kwargs['type'] = tracktype
kwargs['longLabel'] = kwargs.get('longLabel', long_label)
kwargs['shortLabel'] = kwargs.get('shortLabel', short_label)
self.kwargs = kwargs
self._orig_kwargs = kwargs.copy()
def __init__(self, genome, trackdb=None, genome_file_obj=None):
"""
Represents a 2-line genome stanza within a "genomes.txt" file.
The file itself is represented by a :class:`GenomesFile` object.
"""
HubComponent.__init__(self)
self.genome = genome
self.trackdb = None
if trackdb is not None:
self.add_trackdb(trackdb)
if genome_file_obj:
self.add_parent(genome_file_obj)
def __init__(self, genome, trackdb=None, genome_file_obj=None):
"""
Represents a 2-line genome stanza within a "genomes.txt" file.
The file itself is represented by a :class:`GenomesFile` object.
"""
HubComponent.__init__(self)
self.genome = genome
self.trackdb = None
if trackdb is not None:
self.add_trackdb(trackdb)
if genome_file_obj:
self.add_parent(genome_file_obj)
def __init__(self, trackdbs=None):
"""
Represents the file containing one or more include trackDb.* lines
"""
HubComponent.__init__(self)
if trackdbs is None:
trackdbs = []
self._trackdbs = []
for trackdb in trackdbs:
self.add_trackdbs(trackdb)
self._local_fn = None
self._remote_fn = None
def __init__(self, tracks=None):
"""
Represents the file containing one or more Track objects (which each
represent a stanza).
"""
HubComponent.__init__(self)
if tracks is None:
tracks = []
self._tracks = []
for track in tracks:
self.add_track(track)
self._local_fn = None
self._remote_fn = None
def __init__(self, tracks=None):
"""
Represents the file containing one or more Track objects (which each
represent a stanza).
"""
HubComponent.__init__(self)
if tracks is None:
tracks = []
self._tracks = []
for track in tracks:
self.add_track(track)
self._local_fn = None
self._remote_fn = None
def __init__(self, genome=None):
"""
Represents the genomes file on disk. Can contain multiple
:class:`Genome` objects, each of which represent a stanza in this
file.
The file ultimately created (with the self.render() method) will be
determined by the parent Hub's `genome_filename` attribute. By
default, this is the hub name, plus ".genomes.txt"
"""
HubComponent.__init__(self)
self._local_fn = None
self._remote_fn = None
self.genomes = []
if genome is None:
genome = []
for genome in genome:
self.add_genome(genome)
def __init__(self, genome=None):
"""
Represents the genomes file on disk. Can contain multiple
:class:`Genome` objects, each of which represent a stanza in this
file.
The file ultimately created (with the self.render() method) will be
determined by the parent Hub's `genome_filename` attribute. By
default, this is the hub name, plus ".genomes.txt"
"""
HubComponent.__init__(self)
self._local_fn = None
self._remote_fn = None
self.genomes = []
if genome is None:
genome = []
for genome in genome:
self.add_genome(genome)
def __init__(self, hub, short_label="", long_label=None,
genomes_file=None, genomes_filename=None, email="",
url=None):
"""
Represents a top-level track hub container.
"""
HubComponent.__init__(self)
self.url = url
self._local_fn = None
self._remote_fn = None
self._local_dir = None
self._remote_dir = None
self.hub = hub
self.short_label = short_label
if not long_label:
long_label = short_label
self.long_label = long_label
self.email = email
self.genomes_file = None
if genomes_file is not None:
self.add_genomes_file(genomes_file)
def __init__(self, groups):
HubComponent.__init__(self)
self._local_fn = None
self._remote_fn = None
self.groups = []
self.add_groups(groups)
def __init__(self,
name,
tracktype=None,
short_label=None,
long_label=None,
subgroups=None,
local_fn=None,
remote_fn=None,
html_string=None,
**kwargs):
"""
Represents a single track stanza.
:param name: String; name of the track
:param tracktype: String; type of the track (e.g., "bam")
:param url: String; full URL for the track (i.e., bigDataUrl)
:param short_label: String; used for the left-hand side track label
:param long_label:
String; used for the longer middle labels; if None will copy
short_label
:param subgroups:
A dictionary of `{name: tag}` where each `name` is the name of
a SubGroupDefinition in a parent :class:`CompositeTrack` and each
`tag` is a key in the SubGroupDefinition.mapping dictionary. They
end up looking like this in the string representation::
subGroups view=aln celltype=ES
:param local_fn:
String; Local path to the file (used for uploading)
:param remote_fn:
String; path to upload the file to, over rsync and ssh.
"""
HubComponent.__init__(self)
_check_name(name)
self.name = name
self.tracktype = tracktype
if short_label is None:
short_label = name
self.short_label = short_label
if long_label is None:
long_label = short_label
self.long_label = long_label
self._local_fn = local_fn
self._remote_fn = remote_fn
self.html_string = html_string
self.subgroups = {}
self.add_subgroups(subgroups)
# Convert pythonic strings to UCSC versions
kwargs['track'] = name
kwargs['type'] = tracktype
kwargs['longLabel'] = kwargs.get('longLabel', long_label)
kwargs['shortLabel'] = kwargs.get('shortLabel', short_label)
self.kwargs = kwargs
self._orig_kwargs = kwargs.copy()
def __init__(self, groups):
HubComponent.__init__(self)
self._local_fn = None
self._remote_fn = None
self.groups = []
self.add_groups(groups)
