DNA Features Viewer

DNA Features Viewer

from dna_features_viewer import GraphicFeature, GraphicRecord
features=[
    GraphicFeature(start=0, end=20, strand=+1, color="#ffd700",
                   label="Small feature"),
    GraphicFeature(start=20, end=500, strand=+1, color="#ffcccc",
                   label="Gene 1 with a very long name"),
    GraphicFeature(start=400, end=700, strand=-1, color="#cffccc",
                   label="Gene 2"),
    GraphicFeature(start=600, end=900, strand=+1, color="#ccccff",
                   label="Gene 3")
]
record = GraphicRecord(sequence_length=1000, features=features)
record.plot(figure_width=5)

image.png

如果我们在上面的代码中用 CircularGraphicRecord 替换 GraphicRecord，我们会得到一个构造的圆形图:

image.png

通过使用 plot _ with _ bokeh 代替 plot，也可以生成交互式(基于浏览器的)图形:

image.png

DNA 特性浏览器允许在记录图下绘制核苷酸或氨基酸序列:

from dna_features_viewer import GraphicFeature, GraphicRecord

sequence = "ATGCATGCATGCATGCATGCATGCATGC"
record = GraphicRecord(sequence=sequence, features=[
    GraphicFeature(start=5, end=10, strand=+1, color='#ffcccc'),
    GraphicFeature(start=8, end=15, strand=+1, color='#ccccff')
])

ax, _ = record.plot(figure_width=5)
record.plot_sequence(ax)
record.plot_translation(ax, (8, 23), fontdict={'weight': 'bold'})
ax.figure.savefig('sequence_and_translation.png', bbox_inches='tight')

image.png

Edinburgh-Genome-Foundry/DnaFeaturesViewer: Python library to plot DNA sequence features (e.g. from Genbank files) (github.com)