higlass / higlass/higlass-python
Local BAM files
- 主要言語
- Python
- スター
- 66
- フォーク
- 11
- PR マージ指標
- 30日以内にマージされた PR はありません
説明
```
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.
コントリビューションガイド
調査の方向性
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.
索引モデルが issue の本文から書いたものです。
評価
- 技術スタック
- jupyter-notebook, python
- 領域
- backend, bioinformatics
- issue の種類
- 機能追加
- 難易度
- 4/5
- 見積もり時間
- 3〜5日
- 活発さ
- 停滞
- 明瞭さ
- おおむね明確
- 初心者へのやさしさ
- 35/100