Annotation DB Features

Genomic annotations can be visualised directly from an annotation database, without needing a sequence object. This is useful for exploring annotations loaded from GFF or GenBank files.

Drawing features from an annotation database

We load annotations for Caenorhabditis elegans chromosome I from a GFF file.

from cogent3 import load_annotations, draw_annotations

db = load_annotations(path="data/C-elegans-chromosome-I.gff")
db

GffAnnotationDb(source=':memory:', total_records=60166)

Drawing all features for a region

We can draw features for a specific region by providing coordinate bounds.

fig = draw_annotations(db, seqid="I", biotype=("gene", "CDS"), start=25000, stop=35000)
fig.show(height=400, width=700)

Note

This produces the same visual output as seq.get_drawable(biotype=...), but without loading the sequence data.

Using the range slider

By default, figures include an interactive range slider below the main plot. Drag the handles or select a region on the slider to zoom into a portion of the sequence. The x-axis label indicates the slider.

Note

Hover over filled shapes to see feature details (name, biotype, coordinates, strand).

Filtering by biotype

We can select specific feature types to display.

fig = draw_annotations(db, seqid="I", biotype="gene", start=25000, stop=35000)
fig.show(height=300, width=650)

Disabling the range slider for static images

The range slider is included when saving figures as images. To produce a clean static image, disable the controls with show_controls=False.

fig = draw_annotations(db, seqid="I", biotype="gene", start=25000, stop=35000, show_controls=False)
fig.show(height=300, width=650)