higlass / higlass/higlass-python
Support (inline) bedlike data
- Lenguaje dominante
- Python
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- 66
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Descripción
```
Bed-like data
-------------
If you have data representing intervals in a Python object, you can load it
directly into higlass using the `bedtiles` helper function:
.. image:: img/beditems.png
.. code-block:: python
from higlass.client import View, Track
from higlass.inline_tiles import bedtiles
import higlass
bed = [['chr1', 1000, 2000, 'item #1', '.', '+'],
['chr2', 3000, 3500, 'item #1', '.', '-']]
chroms = [['chr1', 2100], ['chr2', 4000]]
data = bedtiles(bed, chroms)
track = Track(track_type='bedlike', position='top',
height=50, data=data, options={"minusStrandColor": "red"})
d,s,v = higlass.display([[track]])
d
Note that this function loads all the data into the viewconf and does
not use a server. Do not use this function with more than ~3000 items of
data.
```
We haven't implemented an inline-tiles function, however this API should be easy to support.
Guía de contribución
Línea de trabajo
Start in higlass/inline_tiles.py with the existing bedtiles helper and review how its data is passed to a bedlike Track. Support the inline-tiles API for the documented bed-like Python data, then verify that the sample with chromosome lengths and strand colors can be displayed without a server.
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Evaluación
- Stack tecnológico
- python
- Área
- data-visualization
- Tipo de issue
- Nueva funcionalidad
- Dificultad
- 2/5
- Tiempo estimado
- 1-3 horas
- Estado de actividad
- Estancado
- Claridad
- Bastante claro
- Aptitud para principiantes
- 52/100