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bgoncotree-0.5
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BBGLab interface for an OncoTree
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bgoncotree-0.5 |
| نام | bgoncotree |
| نسخه کتابخانه | 0.5 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Barcelona Biomedical Genomics Lab |
| ایمیل نویسنده | bbglab@irbbarcelona.org |
| آدرس صفحه اصلی | https://bitbucket.org/bgframework/bgoncotree |
| آدرس اینترنتی | https://pypi.org/project/bgoncotree/ |
| مجوز | Apache Software License 2.0 |
BGOncoTree
==========
.. |ot| replace:: **BGOncoTree**
.. |tree| replace:: *oncotree*
|ot| is a Python package to standardize the use of the OncoTree within the BBGLab.
Installation
------------
|ot| works with Python 3.5+ and can be installed with pip::
pip install bgoncotree
Usage
-----
Any use of |ot| requires to initialize the tree:
.. code:: python
from bgoncotree.main import BGOncoTree
tree = BGOncoTree()
|ot| accepts a file as argument if you want to `provide your own tree`_.
Each node is composed by:
- ``id``: short identifier of the node (e.g. ``ALL``)
- ``parent``: ancestor node
- ``children``: list of descendent nodes
- ``synonyms``: list of alternative names that can be used to search for this node
- ``name``: first provided synonym or node id
Python
******
The first thing to do is **initialize** the *BGOncoTree* object:
.. code:: python
tree = BGOncoTree()
The *BGOncoTree* object is a *dictionary* that you can query to **get
each node**:
.. code:: python
node = tree['CANCER']
Using the ID of the node or any synonym you can ``find`` the node:
.. code:: python
node = tree.find('clear cell sarcoma')
To **explore** the tree, you can use the ``iter_from`` method:
.. code:: python
for node, level in tree.iter_from(tree['ALL'], descending=True):
...
The `level` is simply an integer indicating the level of nested with respect
to the ``starting_node``.
If you want to explore the full tree, you can get the **root node** as:
.. code:: python
root_node = tree.root
The methods ``descendants`` and ``ancestors`` do the same as ``iter_from``
but you do not need to indicate the ``descending`` flag, the ``level`` is not
returned and node can also be a string. E.g.:
.. code:: python
for node in tree.descendants('ALL'):
...
.. important:: `iter_from``, ``descendants`` and ``ancestors`` methods
return the starting node.
There are two other methods that you can make use of.
``search`` can be used to **search** for all nodes containing a word
in their names. E.g.:
.. code:: python
for node in tree.search('acute'):
...
The ``get`` method is useful if you expect only one result from a search.
E.g.:
.. code:: python
node = tree.get('Cholangiocarcinoma')
This method will raise an exception if none or more than 1 items are found.
Command line
************
The command line provides two utilities to explore the tree
``bgoncotree ancestors`` and ``bgoncotree descendants``.
Output can be formatted in json, and you can also set a recursion limit.
See first one level of childs of ``HEMATO`` node:
.. code:: bash
bgoncotree descendants --node HEMATO --json --limit 2
In addition, the same ``search`` function as in Python can be called
from the command line as::
bgoncotree search acute
Tab completion can be enabled adding
``eval "$(_BGONCOTREE_COMPLETE=source bgoncotree)"`` to your ``.bashrc``
file as explained in the
`bash completion section of Click <https://click.palletsprojects.com/en/7.x/bashcomplete/>`_
.. _provide your own tree:
Defining your own tree
----------------------
|ot| uses `bgdata <https://pypi.org/project/bgdata/>`_ to get the most recent
version of the |tree| used in the lab.
However, you can pass a file with your own |tree|::
from bgoncotree.main import BGOncoTree
tree = BGOncoTree(file)
If you are interested in creating your own |tree|,
you need a ``tsv`` file with 2 columns: ``ID`` and ``PARENT``.
Each node can only have 1 parent, and there must but one node without a
parent: the root node.
You can provide an additional extra column ``NAMES`` with a comma separated
list of synonyms for each node. The first name will be used as the
name to display.
You can **validate** your tree using the command line::
bgoncotree validate my_tree.tsv
نیازمندی
| مقدار | نام |
|---|---|
| >=2 | bgdata |
| - | click |
نحوه نصب
نصب پکیج whl bgoncotree-0.5:
pip install bgoncotree-0.5.whl
نصب پکیج tar.gz bgoncotree-0.5:
pip install bgoncotree-0.5.tar.gz