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cytopast-1.1.1
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مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشتر
تبلیغات ما
مشتریان به طور فزاینده ای آنلاین هستند. تبلیغات می تواند به آنها کمک کند تا کسب و کار شما را پیدا کنند.
مشاهده بیشترتوضیحات
Visualisation of PastML trees.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | cytopast-1.1.1 |
| نام | cytopast |
| نسخه کتابخانه | 1.1.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Anna Zhukova |
| ایمیل نویسنده | anna.zhukova@pasteur.fr |
| آدرس صفحه اصلی | https://github.com/evolbioinfo/cytopast |
| آدرس اینترنتی | https://pypi.org/project/cytopast/ |
| مجوز | - |
# 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 :)
نحوه نصب
نصب پکیج whl cytopast-1.1.1:
pip install cytopast-1.1.1.whl
نصب پکیج tar.gz cytopast-1.1.1:
pip install cytopast-1.1.1.tar.gz