higlass / higlass/higlass-python

Local BAM files

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Dominant language
Python
Stars
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Forks
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Description

```

BAM Files
---------

View sequencing read mappings. First we must load the `higlass-pileup plugin track `_
as a ``hg.PluginTrack``:

.. code-block:: python

%%javascript

require(["https://unpkg.com/higlass-pileup/dist/higlass-pileup.min.js"],
function(hglib) {

});

And then we can view pileups:

.. code-block:: python

import higlass
from higlass.tilesets import Tileset, bam
from higlass.client import Track, View

filename = '../data/ont.10K.bam'
indexfile = '../data/ont.10K.bam.bai'

bam_ts = bam(filename, indexfile)

display, server, viewconf = higlass.display(
[View([
Track('top-axis', height=20),
Track(track_type="pileup",
position='top', tileset=bam_ts, height=50 )
], initialXDomain = [
0,
2000
])]
)
display

.. image:: img/jupyter-pileup-no-code.png

```

Usage of the BAM files is shown in the plugin documentation, but we don't currently support local files and would need to extend the server.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Read the higlass-pileup plugin documentation and compare its BAM example with the Python `bam(filename, indexfile)` usage shown here. Then trace the server extension needed for local files; done means the local BAM and `.bai` example renders a pileup as shown.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, python
Domain
backend, bioinformatics
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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