igv-jupyterlab 1.0.1
igv-jupyterlab is an extension for Jupyter Lab and traditional Jupyter Notebooks which wraps igv.js.
License: BSD
Requires Python: >=3.8
Keywords: Jupyter,Widgets,IPython

# igv-jupyterlab

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igv-jupyterlab is an extension for Jupyter Lab and traditional Jupyter Notebooks which wraps igv.js.

## Installation

You can install using `pip`:

```bash
pip install igv_jupyterlab
```

If you are using Jupyter Notebook 5.2 or earlier, you may also need to enable
the nbextension:
```bash
jupyter nbextension enable --py [--sys-prefix|--user|--system] igv_jupyterlab
```

## Usage

This extension provides a python wrapper which allows you render igv.js 
in a cell and call its API from the notebook.

### Initialization

To insert an IGV instance into a cell: 

```python
from igv_jupyterlab import IGV

# At minimum, IGV requires a single argument, genome.

# For supported genomes, a simple name may be supplied.
IGV(genome="hg19")

# For all other genomes, we must construct a configuration object.
# A helper method supplied to make this easier.
genome = IGV.create_genome(
    name="Human (GRCh38/hg38)",
    fasta_url="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",
    index_url="https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",
    cytoband_url="https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/cytoBandIdeo.txt",
)

igv = IGV(genome=genome)

display(igv)
```

Supported genomes are [listed here](https://s3.amazonaws.com/igv.org.genomes/genomes.json).
Reference configuration is described in the [igv.js documentation](https://github.com/igvteam/igv.js/wiki/Reference-Genome).

```python
# It is also easy to change the genome to something else
some_other_genome = igv.create_genome(...)

igv.load_genome(some_other_genome)
```

### Tracks

To load a track pass a track configuration object to load_track().  Track configuration
objects are described in the [igv.js documentation](https://github.com/igvteam/igv.js/wiki/Tracks-2.0).

#### Remote URL

```python
track = IGV.create_track(
    name="Segmented CN",
    url="https://data.broadinstitute.org/igvdata/test/igv-web/segmented_data_080520.seg.gz",
    format="seg",
    indexed=False
)

igv.load_track(track)
```

#### Local File

Tracks can be loaded from local files using the Jupyter web server by prepending "tree" to the path.

```python
track = IGV.create_track(
    name="Local VCF",
    url="/tree/absolute/path/to/example.vcf",
    format="vcf",
    type="variant",
    indexed=False
)

igv.load_track(track)
```

#### Remove a track

```python

# It is easy to remove a track by name
igv.remove_track("HG00103")
```

### Navigation

Zoom in by a factor of 2

```python
igv.zoom_in()
```

Zoom out by a factor of 2

```python
igv.zoom_out()
```

Jump to a specific locus

```python
igv.locus = 'chr1:3000-4000'

# A helper method is available to avoid having to perform string formatting
igv.search_locus('chr1', 3000, 4000)
```

Jump to a specific gene. This uses the IGV search web service, which currently supports a limited number of genomes:  hg38, hg19, and mm10.
To configure a custom search service see the [igv.js documentation](https://github.com/igvteam/igv.js/wiki/Browser-Configuration-2.0#search-object-details)

```python
igv.locus = 'myc'
```

### SVG output

Displaying the current IGV view as an SVG is simple - and only requires one call now!  

```python
igv.get_svg()
```


## Development Installation

Create a dev environment:
```bash
conda create -n igv_jupyterlab-dev -c conda-forge nodejs yarn python jupyterlab
conda activate igv_jupyterlab-dev
```

Install the python. This will also build the TS package.
```bash
pip install -e ".[test, examples]"
```

When developing your extensions, you need to manually enable your extensions with the
notebook / lab frontend. For lab, this is done by the command:

```
jupyter labextension develop --overwrite .
yarn run build
```

For classic notebook, you need to run:

```
jupyter nbextension install --sys-prefix --symlink --overwrite --py igv_jupyterlab
jupyter nbextension enable --sys-prefix --py igv_jupyterlab
```

Note that the `--symlink` flag doesn't work on Windows, so you will here have to run
the `install` command every time that you rebuild your extension. For certain installations
you might also need another flag instead of `--sys-prefix`, but we won't cover the meaning
of those flags here.

### How to see your changes
#### Typescript:
If you use JupyterLab to develop then you can watch the source directory and run JupyterLab at the same time in different
terminals to watch for changes in the extension's source and automatically rebuild the widget.

```bash
# Watch the source directory in one terminal, automatically rebuilding when needed
yarn run watch
# Run JupyterLab in another terminal
jupyter lab
```

After a change wait for the build to finish and then refresh your browser and the changes should take effect.

#### Python:
If you make a change to the python code then you will need to restart the notebook kernel to have it take effect.