higlass / higlass/higlass-python
Local BAM files
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- Dominant language
- Python
- Stars
- 66
- Forks
- 11
- PR merge metrics
- No merged PRs in 30d
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
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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