EIYBrowse.tracks.interval module

The interval module provides a track for displaying discrete genomic features, or intervals, such as those you might find in a bed file.

Whilst the UCSC browser treats genes as a specialized case of intervals, we have a separate track for genes: EIYBrowse.tracks.genes.

class EIYBrowse.tracks.interval.GenomicIntervalTrack(datafile, labels=None, glyphs=None, name=None, name_rotate=False)

Bases: EIYBrowse.tracks.base.FileTrack

Track for displaying a discrete signal (e.g. a bed file of binding peaks) accross a genomic region

To create a new genomic interval track:

Parameters:

• datafile – Datafile object which will handles access to the genomic intervals across a specific region.
• labels (dict or None) – If specified, a dictionary of additional arguments to pass to matplotlib.pyplot.text()
• glyphs (dict or None) – If specified, a dictionary of additional arguments to pass to matplotlib.axes.AxesSubplot.hlines()
• name (str) – Optional name label
• name_rotate (bool) – Whether to rotate the name label 90 degrees

get_config(region, browser)

Calculate how many rows of height need to be requested.

Parameters:

• region (pybedtools.Interval) – Genomic region to plot
• browser (Browser) – Browser object calling get_config function