from dna_features_viewer import BiopythonTranslator
class MyCustomTranslator(BiopythonTranslator):
"""Custom translator implementing the following theme:
- Color terminators in green, CDS in blue, all other features in gold.
- Do not display features that are restriction sites unless they are BamHI
- Do not display labels for restriction sites.
- For CDS labels just write "CDS here" instead of the name of the gene.
"""
def compute_feature_color(self, feature):
if feature.type == "CDS":
return "blue"
elif feature.type == "terminator":
return "green"
else:
return "gold"
def compute_feature_label(self, feature):
if feature.type == 'restriction_site':
return None
elif feature.type == "CDS":
return "CDS here"
else:
return BiopythonTranslator.compute_feature_label(self, feature)
def compute_filtered_features(self, features):
"""Do not display promoters. Just because."""
return [
feature for feature in features
if (feature.type != "restriction_site")
or ("BamHI" in str(feature.qualifiers.get("label", '')))
]
graphic_record = MyCustomTranslator().translate_record("example_sequence.gb")
ax, _ = graphic_record.plot(figure_width=10)
ax.figure.tight_layout()
ax.figure.savefig("custom_biopython_translator.png")
