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bgsignature-0.2
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مشاهده بیشترتوضیحات
Compute genome signatures
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | bgsignature-0.2 |
| نام | bgsignature |
| نسخه کتابخانه | 0.2 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Barcelona Biomedical Genomics Lab |
| ایمیل نویسنده | bbglab@irbbarcelona.org |
| آدرس صفحه اصلی | https://bitbucket.org/bgframework/bgsignature |
| آدرس اینترنتی | https://pypi.org/project/bgsignature/ |
| مجوز | Apache Software License 2.0 |
.. |bs| replace:: **bgsignature**
BGSignature
===========
|bs| is a package used to compute signatures.
The most basic type of computation is the computation
of the counts of the different k-mers (e.g. 3 or 5).
This computation can be done for a set of mutations,
for a set of regions or for a set of mutation
that fall within certain regions.
|bs| consists of 3 tools:
- **count**: count different k-mers
- **frequency**: divide the counts by the total counts
- **normalize**: divide the counts by counts obtained
separately and normalize the results.
**Advanced features** include:
- ability to group the counts (e.g. group mutations by sample)
- normalize the counts by the context taken from a regions file
- collapse (add together) reverse complementary sequences
Installation
------------
This project is a Python package
and can be installed with ``pip``.
Download the source code, get into this
project directory and execute:
.. code:: bash
pip install .
Usage
-----
Command line interface
**********************
The 3 tools can be called using
- *bgsignature count*
- *bgsignature frequency*
- *bgsignature normalize*
Some examples:
- getting help:
.. code:: bash
bgsignature -h
bgsignature frequency -h
- count triplets in mutation that fall in certain regions using hg38:
.. code:: bash
bgsignature count -m my/muts/file -r my/regions/file
-g hg38 -o my/output.json --cores 4
Python
******
Alternative, the command line options have an equivalent in Python:
.. code:: python
from bgsignature import count, relative_frequency, normalize
that accept similar parameters except the output.
The return object can be used as a dictionary.
If you already have your files loaded in Python
you can use directly count function
in the corresponding module.
E.g.:
.. code:: python
from bgsignature.count import mutation
mutation.count(mutations, 'hg38', 3)
In addition, you can also
use the the "low-level" functions that
do the count (``count_all``
and ``count_group``)
which are much simple and do not
perform any kind of parallelization.
E.g.:
.. code:: python
from bgsignature.count import mutation
mutation.count_all(mutations, 'hg38', 3)
# or to group mutations by sample
mutation.count_group(mutations, 'hg38', 3, 'SAMPLE')
The return object can be normalized to 1,
using the ``sum1()`` method
or divided by some normalization counts
using the ``normalize()`` method.
Important
---------
There are some behavioural characteristics that
must be taken into account:
- |bs| filters out mutations whose reference nucleotide
(as provided in the file), and the
corresponding one in the reference genome do not match.
- when using the ``collapse`` option (enabled by default),
|bs| does not remove one of the collapsed sequences but keeps both.
This means that you need to manually remove the ones you
are not interested in.
- when using ``bgsignature.count.mutation.count``
or ``bgsignature.count.region.count`` function
and a number of ``cores`` for paralelization,
the ``chunk`` parameter must be selected
adequately, as a it can have a huge impact on performance.
File formats
------------
Mutations file
**************
Tab separated file
(can be compressed into ``gz``, ``bgz`` or ``xz`` formats)
with a header and at least these columns:
``CHROMOSOME``, ``POSITION``, ``REF``, ``ALT``.
In addition, ``SAMPLE``, ``CANCER_TYPE`` and ``SIGNATURE``
are optional columns that can be used for
grouping the signature.
Regions file
************
Tab separated file
(can be compressed into ``gz``, ``bgz`` or ``xz`` formats)
with a header and at least these columns:
``CHROMOSOME``, ``START``, ``END``, ``ELEMENT``.
In addition, ``SYMBOL``, and ``SEGMENT``
are optional columns that can be used for
grouping the signature.
Support
-------
If you are having issues, please let us know.
You can contact us at: bbglab@irbbarcelona.org
نحوه نصب
نصب پکیج whl bgsignature-0.2:
pip install bgsignature-0.2.whl
نصب پکیج tar.gz bgsignature-0.2:
pip install bgsignature-0.2.tar.gz