jeff-k / genetracks

Diagrams for genomic sequences

genetracks

Generate track diagrams for genomic alignments

see examples/Genetracks.ipynb for use cases

Example

from genetracks import Figure, Track
import pysam
import sys

f = Figure()

for alignment in pysam.AlignmentFile(sys.argv[1]):
  f.add(Track(alignment.query_start, alignment.query_end))

f.show(w=900).save_svg("alignment.svg")

JSON serialisation

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genetracks's Issues

Simplify coverage plots

I created a subclass of Coverage in the MiCall project. It simplifies the coverage plots by joining all the rectangles that are within 10% of the starting coverage value. That reduces most SVG file sizes to less than 10% of their current size.

Let me know if you like the technique, and I'll create a pull request for you to put this feature in Coverage. The next class in that file is ShadedCoverage to set colour based on coverage depth. You're welcome to that as well, but it might not be as generally useful. It also introduces a matplotlib dependency, although I could probably work around that if needed.

I hope your adventure is not too adventurous. Talk to you later.

Vertical padding ignores track height

How are things, Jeff? I ran into a quirk in the interface for this library.

If you increase the height of a track, the default vertical position doesn't adjust.

Here's an example:

from genetracks import Figure, Track

f = Figure()
f.add(Track(100, 200, label='Foo'))
f.add(Track(10, 90, h=50, label='Bar'))
drawing = f.show()
with open('test.png', 'wb') as f:
    drawing.rasterize(f)

That produces this diagram, where the Bar track is colliding with the Foo track.

I can work around it with the padding parameter, but I'd rather fix the default position. I'll create a pull request for you.

from genetracks import Figure, Track

f = Figure()
f.add(Track(100, 200, label='Foo'))
f.add(Track(10, 90, h=50, label='Bar'), padding=50)
drawing = f.show()
with open('test.png', 'wb') as f:
    drawing.rasterize(f)

That makes it look like this:

Adjust text anchor of labels

We've run into problems with short tracks near the left or right edges. If the label is longer than the track rectangle, then the label text can flow past the edge of the diagram.

Here's an example, including our current workaround:

from genetracks import Figure, Track, Multitrack

f = Figure()

f.add(Track(1, 1500, label='Track with a long contig'))

# The problem
f.add(Track(1, 150, label='Track with a long name'))

# A workaround
f.add(Multitrack([Track(1, 150),
                  Track(1,
                        1500,
                        label='Short track with centred name',
                        color='none')]))

f.show(w=900).saveSvg("alignment.svg")

Here's how it looks:

I thought it might be helpful to set the text-anchor attribute of the labels. I don't think there's a good way to estimate the width of the text, so the best I could think of was to use start when the track starts on the left third of the diagram, middle when it starts in the middle third, and end when it starts on the right third.

If you think that's a reasonable approach, I can prepare a pull request.