def locations_to_biopython_features(
self,
feature_type="misc_feature",
color="red",
label_prefix="",
merge_overlapping=False,
):
"""Return a list of locations (of breach/suboptimality) as annotations.
Parameters
----------
feature_type
Genbank type of the annotations
color
Color property attached to the annotations
label_prefix
The locations will be labelled of the form
"prefix NameOfSpecification()"
merge_overlapping
If true, then overlapping locations (0-5, 2-9) will be merged into a
single one (0-9).
"""
locations = self.locations
if merge_overlapping:
locations = Location.merge_overlapping_locations(locations)
return [
SeqFeature(
location.to_biopython_location(),
type=feature_type,
qualifiers=dict(
label=label_prefix + " " + str(self.specification),
color=color,
),
) for location in locations
]
def locations_as_features(
self,
features_type="misc_feature",
with_specifications=True,
label_prefix="From",
colors="cycle",
merge_overlapping=False,
locations_filter=None,
):
"""Return all locations from all evaluations as biopython features.
Parameters
----------
features_type
The Genbank feature type
with_specifications
If True, features are added to the list to indicate the scope of the
different specifications. If false, only the specification breaches
are returned.
label_prefix
Each breach may be labeled "prefix NameOfSpec(props)", for instance,
"From AvoidPattern(100-200)", to indicate where the breach belongs.
colors
Either a list of colors (one for each specification), e.g.
['red', '#7aab71', ...] or "cycle" for cycling through predefined
colors. The colors are applied to all breaches.
locations_filter
A function (location => True/False) deciding whether
"""
if colors == "cycle":
cycle = colors_cycle(
lightness_factor=self.color_lightness,
color_shift=self.color_shift,
)
colors = [next(cycle) for ev in self.evaluations]
features = [
location.to_biopython_feature(
feature_type="misc_feature",
label=" ".join([
label_prefix,
ev.specification.label(use_short_form=True,
with_location=False),
]),
color=color,
ApEinfo_fwdcolor=color,
ApEinfo_revcolor=color,
) for (ev, color) in zip(self.evaluations_with_locations(), colors)
for location in (Location.merge_overlapping_locations(ev.locations)
if merge_overlapping else ev.locations)
if (locations_filter is None) or locations_filter(location)
]
if with_specifications:
features += [
ev.specification.to_biopython_feature(
feature_type="misc_feature",
label=ev.specification.label(use_short_form=True,
with_location=False),
role=self.specifications_role,
color=color,
ApEinfo_fwdcolor=color,
ApEinfo_revcolor=color,
) for ev, color in zip(self.evaluations, colors)
if ev.specification.__dict__.get("location", False)
]
return features