cytopast 1.1.1

# cytopast

__cytopast__ is a python3 module that creates zoomable HTML visualisation of phylogenetic trees with annotated nodes.

Given a tree and its node annotations, it can either visualise them as-is,
or apply [PastML](https://github.com/saishikawa/PASTML) to infer ancestral states based on the tip states.

The states are visualised as different colours of the tree nodes using [Cytoscape.js](http://js.cytoscape.org/)

# Article

For a detailed description of PastML/cytopast: see Ishikawa SA, Zhukova A, Iwasaki W, Gascuel O (2018) __A Fast Likelihood Method to Reconstruct and Visualize Ancestral Scenarios__ [[bioRxiv]](https://doi.org/10.1101/379529).

# Input data
As an input, one needs to provide a **rooted** phylogenetical tree in [newick](https://en.wikipedia.org/wiki/Newick_format) format,
and a table containing tip states,
in tab-delimited (by default) or csv format (to be specified with *--data_sep ,* option).

### Example
You can download [HIV1-A in Albania data](examples/Albania/data) as an example.
Let's assume that the tree and annotation files are in the Downloads folder,
and are named respectively Albanian.tree.152tax.tre and data.txt.

The data.txt is a comma-separated file, containing tip ids in the first column,
and Country in the second column, i.e.:

id | Country
----- | -----
98CMAJ6932 | Africa
98CMAJ6933 | Africa
96CMAJ6134 | Africa
00SEAY5240 | WestEurope
... | ...
02GRAY0303 | Greece
97YUAF9960 | EastEurope

# Try it online
Try it at [pastml.pasteur.fr](https://pastml.pasteur.fr)

# Run it on your computer

There are 2 alternative ways to run cytopast on your computer: with [docker](https://www.docker.com/community-edition), or in python3.

## Run with docker

### Basic usage
Once [docker](https://www.docker.com/community-edition) is installed, run the following command:

```bash
docker run -v <path_to_the_folder_containing_the_tree_and_the_annotations>:/data:rw -t evolbioinfo/pastml --tree /data/<tree_file> --data /data/<annotation_file> --data_sep <separator_eg_comma> --columns <one_or_more_column_names> --html_compressed /data/<map_name>
```

For example, to reconstruct and visualise the ancestral Country states for Albanian data,
one needs to run the following command:

```bash
docker run -v ~/Downloads:/data:rw -t evolbioinfo/pastml --tree /data/Albanian.tree.152tax.tre --data /data/data.txt --data_sep , --columns Country --html_compressed /data/Albanian_map.html
```

This will produce a file Albanian_map.html in the Downloads folder,
that can be viewed with a browser.


### Help

To see advanced options, run
```bash
docker run -t evolbioinfo/pastml -h
```

## Run in python3

### Windows
For **Windows** users, we recommend installing cytopast via [Cygwin environment](https://www.cygwin.com/).
First instal gcc, gsl, python3 and pip3 from the Cygwin packages. Then install cytopast:
```bash
pip3 install cytopast
```

### All other platforms

We strongly recommend installing cytopast for python via [conda](https://conda.io/docs/), following the procedure described below:

#### Installing with conda

Once you have conda installed create an environment for cytopast with python3, gcc and gsl:

```bash
conda create --name cytopast python=3 gcc gsl
```

Then activate it:
```bash
source activate cytopast
```

Then install cytopast in it:

```bash
pip install cytopast
```

#### Installing without conda

Install [GNU GSL](https://www.gnu.org/software/gsl/), following the instructions provided on GSL website.

Then install cytopast:

```bash
pip3 install cytopast
```

### Basic usage in a command line
If you installed cytopast via conda, do not forget to first activate the dedicated environment, e.g.

```bash
source activate cytopast
```

To run cytopast:

```bash
cytopast --tree <path/to/tree_file.nwk> --data <path/to/annotation_file.tab> --columns <one_or_more_column_names> --html_compressed <path/to/output/map.html> --data_sep <separator_eg_comma>
```

For example, to reconstruct and visualise the ancestral Country states for Albanian data,
one needs to run the following command:

```bash
cytopast --tree ~/Downloads/Albanian.tree.152tax.tre --data ~/Downloads/data.txt --data_sep , --columns Country --html_compressed ~/Downloads/Albanian_map.html
```

This will produce a file Albanian_map.html in the Downloads folder,
that can be viewed with a browser.

### Help

To see advanced options, run:
```bash
cytopast -h
```

### Basic usage in python3
```python
from cytopast.pastml_analyser import pastml_pipeline

# Path to the table containing tip/node annotations, in csv or tab format
data = "~/Downloads/data.txt"

# Path to the tree in newick format
tree = "~/Downloads/Albanian.tree.152tax.tre"

# Columns present in the annotation table,
# for which we want to reconstruct ancestral states
# (for Albanian data we only have one column, but multiple columns are also allowed)
columns = ['Country']

# Path to the output compressed map visualisation
html_compressed = "~/Downloads/Albanian_map.html"

# (Optional) path to the output tree visualisation
html = "~/Downloads/Albanian_tree.html"

pastml_pipeline(data=data, data_sep=',', columns=columns, name_column='Country',
tree=tree,
html_compressed=html_compressed, html=html,
verbose=True)
```

### Examples

See the [examples folder](https://github.com/evolbioinfo/cytopast/tree/master/examples) for ideas :)