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PyMassSpec-2.3.0
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Python Toolkit for Mass Spectrometry
| ویژگی | مقدار |
|---|---|
| سیستم عامل | OS Independent |
| نام فایل | PyMassSpec-2.3.0 |
| نام | PyMassSpec |
| نسخه کتابخانه | 2.3.0 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Dominic Davis-Foster |
| ایمیل نویسنده | dominic@davis-foster.co.uk |
| آدرس صفحه اصلی | https://github.com/domdfcoding/PyMassSpec |
| آدرس اینترنتی | https://pypi.org/project/PyMassSpec/ |
| مجوز | GNU General Public License v2 (GPLv2) |
************
PyMassSpec
************
.. start short_desc
**Python Toolkit for Mass Spectrometry**
.. end short_desc
.. start shields
.. list-table::
:stub-columns: 1
:widths: 10 90
* - Docs
- |docs| |docs_check|
* - Tests
- |travis| |actions_windows| |actions_macos| |coveralls| |codefactor| |pre_commit_ci|
* - PyPI
- |pypi-version| |supported-versions| |supported-implementations| |wheel|
* - Anaconda
- |conda-version| |conda-platform|
* - Activity
- |commits-latest| |commits-since| |maintained|
* - Other
- |license| |language| |requires| |pre_commit|
.. |docs| image:: https://img.shields.io/readthedocs/pymassspec/latest?logo=read-the-docs
:target: https://pymassspec.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Build Status
.. |docs_check| image:: https://github.com/domdfcoding/PyMassSpec/workflows/Docs%20Check/badge.svg
:target: https://github.com/domdfcoding/PyMassSpec/actions?query=workflow%3A%22Docs+Check%22
:alt: Docs Check Status
.. |travis| image:: https://img.shields.io/travis/domdfcoding/PyMassSpec/master?logo=travis
:target: https://travis-ci.org/domdfcoding/PyMassSpec
:alt: Travis Build Status
.. |actions_windows| image:: https://github.com/domdfcoding/PyMassSpec/workflows/Windows%20Tests/badge.svg
:target: https://github.com/domdfcoding/PyMassSpec/actions?query=workflow%3A%22Windows+Tests%22
:alt: Windows Tests Status
.. |actions_macos| image:: https://github.com/domdfcoding/PyMassSpec/workflows/macOS%20Tests/badge.svg
:target: https://github.com/domdfcoding/PyMassSpec/actions?query=workflow%3A%22macOS+Tests%22
:alt: macOS Tests Status
.. |requires| image:: https://requires.io/github/domdfcoding/PyMassSpec/requirements.svg?branch=master
:target: https://requires.io/github/domdfcoding/PyMassSpec/requirements/?branch=master
:alt: Requirements Status
.. |coveralls| image:: https://img.shields.io/coveralls/github/domdfcoding/PyMassSpec/master?logo=coveralls
:target: https://coveralls.io/github/domdfcoding/PyMassSpec?branch=master
:alt: Coverage
.. |codefactor| image:: https://img.shields.io/codefactor/grade/github/domdfcoding/PyMassSpec?logo=codefactor
:target: https://www.codefactor.io/repository/github/domdfcoding/PyMassSpec
:alt: CodeFactor Grade
.. |pypi-version| image:: https://img.shields.io/pypi/v/PyMassSpec
:target: https://pypi.org/project/PyMassSpec/
:alt: PyPI - Package Version
.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/PyMassSpec?logo=python&logoColor=white
:target: https://pypi.org/project/PyMassSpec/
:alt: PyPI - Supported Python Versions
.. |supported-implementations| image:: https://img.shields.io/pypi/implementation/PyMassSpec
:target: https://pypi.org/project/PyMassSpec/
:alt: PyPI - Supported Implementations
.. |wheel| image:: https://img.shields.io/pypi/wheel/PyMassSpec
:target: https://pypi.org/project/PyMassSpec/
:alt: PyPI - Wheel
.. |conda-version| image:: https://img.shields.io/conda/v/domdfcoding/PyMassSpec?logo=anaconda
:target: https://anaconda.org/domdfcoding/PyMassSpec
:alt: Conda - Package Version
.. |conda-platform| image:: https://img.shields.io/conda/pn/domdfcoding/PyMassSpec?label=conda%7Cplatform
:target: https://anaconda.org/domdfcoding/PyMassSpec
:alt: Conda - Platform
.. |license| image:: https://img.shields.io/github/license/domdfcoding/PyMassSpec
:target: https://github.com/domdfcoding/PyMassSpec/blob/master/LICENSE
:alt: License
.. |language| image:: https://img.shields.io/github/languages/top/domdfcoding/PyMassSpec
:alt: GitHub top language
.. |commits-since| image:: https://img.shields.io/github/commits-since/domdfcoding/PyMassSpec/v2.3.0
:target: https://github.com/domdfcoding/PyMassSpec/pulse
:alt: GitHub commits since tagged version
.. |commits-latest| image:: https://img.shields.io/github/last-commit/domdfcoding/PyMassSpec
:target: https://github.com/domdfcoding/PyMassSpec/commit/master
:alt: GitHub last commit
.. |maintained| image:: https://img.shields.io/maintenance/yes/2020
:alt: Maintenance
.. |pre_commit| image:: https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white
:target: https://github.com/pre-commit/pre-commit
:alt: pre-commit
.. |pre_commit_ci| image:: https://results.pre-commit.ci/badge/github/domdfcoding/PyMassSpec/master.svg
:target: https://results.pre-commit.ci/latest/github/domdfcoding/PyMassSpec/master
:alt: pre-commit.ci status
.. end shields
PyMassSpec is a Python_ package for processing gas chromatography-mass spectrometry data.
PyMassSpec provides a framework and a set of components for rapid development and testing of methods for processing of chromatography--mass spectrometry data.
PyMassSpec can be used interactively through the Python shell, in a `Jupyter Notebook <https://jupyter.org/>`_, or the functions can be collected into scripts when it is preferable to perform data processing in the batch mode.
|
Forked from the original PyMS Repository: https://github.com/ma-bio21/pyms.
Originally by Andrew Isaac, Sean O'Callaghan and Vladimir Likić. The original publication can be found here: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-115
The original project seems to have been abandoned as there has been no activity since 2017.
|
.. contents:: Table of Contents
:local:
The PyMassSpec project
=========================
The directory structure of PyMassSpec is as follows:
.. code-block:: text
/
├── pyms: The PyMassSpec code
│
├── pyms-data: Example GC-MS data files
│
├── pyms-demo: Examples of how to use PyMassSpec
│
├── tests: pytest tests
│
└── doc-source: Sphinx source for documentation
Features
=========
Installation
==============
PyMassSpec can be installed with the following command:
.. code-block:: bash
$ pip --user install PyMassSpec
This will also install the following dependencies:
.. code-block:: bash
numpy >= 1.16.2
scipy >= 1.2.1
pymzml >= 2.2.1
matplotlib >= 3.0.2
openpyxl >= 2.6.2
netCDF4 >= 1.5.0
biopython >= 1.74
deprecation >= 2.0.6
PyMassSpec can also make use of 'mpi4py' if it is installed. See https://mpi4py.readthedocs.io/en/stable/ for further information.
Usage
=======
A tutorial illustrating various PyMassSpec features in detail is provided
in subsequent chapters of this User Guide. The commands executed
interactively are grouped together by example, and can be found
`here <https://pymassspec.readthedocs.io/en/master/pyms-demo/introduction.html#pyms-demo>`__.
.. If you are viewing this source, the examples can be found in the pyms-demo directory, and the data files in pyms-data
The data used in the PyMassSpec documentation and examples is available
`here <https://pymassspec.readthedocs.io/en/master/pyms-demo/data-files.html>`__.
In the "`Demos and Examples`_" section there
is a page corresponding to each example, coded with the chapter number
(ie. "``pyms-demo/20a/``" corresponds to the Example 20a, from Chapter 2).
Each example has a script named 'proc.py' which contains the commands given in the example.
These scripts can be run with the following command:
.. code-block:: bash
$ python3 proc.py
Example processing GC-MS data
-------------------------------
Download the file ``gc01_0812_066.jdx`` and save it in the folder ``data``.
This file contains GC-MS data in the the JCAMP-DX format.
First the raw data is loaded:
>>> from pyms.GCMS.IO.JCAMP import JCAMP_reader
>>> jcamp_file = "data/gc01_0812_066.jdx"
>>> data = JCAMP_reader(jcamp_file)
-> Reading JCAMP file 'Data/gc01_0812_066.jdx'
>>> data
<pyms.GCMS.Class.GCMS_data at 0x7f3ec77da0b8>
The intensity matrix object is then built by binning the data:
>>> from pyms.IntensityMatrix import build_intensity_matrix_i
>>> im = build_intensity_matrix_i(data)
In this example, we show how to obtain the dimensions of the
newly created intensity matrix, then loop over all ion chromatograms,
and for each ion chromatogram apply Savitzky-Golay noise filter
and tophat baseline correction:
>>> n_scan, n_mz = im.size
>>> from pyms.Noise.SavitzkyGolay import savitzky_golay
>>> from pyms.TopHat import tophat
>>> for ii in range(n_mz):
... print("working on IC", ii)
... ic = im.get_ic_at_index(ii)
... ic1 = savitzky_golay(ic)
... ic_smooth = savitzky_golay(ic1)
... ic_base = tophat(ic_smooth, struct="1.5m")
... im.set_ic_at_index(ii, ic_base)
The resulting noise and baseline corrected ion chromatogram is saved back into the intensity matrix.
Further examples can be found in the `documentation`_
Contributing
==============
Contributions are very welcome. Tests can be run with `pytest`_.
Please ensure the coverage is at least |coveralls|
before you submit a pull request.
For further information see the section `Contributing to PyMassSpec`_
License
=========
PyMassSpec is Free and Open Source software released under the `GNU General Public License version 2 <GPL_>`__.
Issues
========
If you encounter any problems, please `file an issue`_ along with a
detailed description.
.. _`documentation`: https://pymassspec.readthedocs.io
.. _`Contributing to PyMassSpec`: https://pymassspec.readthedocs.io/en/master/Contributing/Contributing.html
.. _`pytest`: https://pytest.org/
.. _`file an issue`: https://github.com/domdfcoding/pymassspec/issues
.. _Python: https://www.python.org/
.. _GPL: https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html
.. _Demos and Examples: https://pymassspec.readthedocs.io/en/master/pyms-demo/introduction.html#pyms-demo
نیازمندی
| مقدار | نام |
|---|---|
| >=1.74 | biopython |
| >=2.1.0 | deprecation |
| >=1.2.0 | domdf-python-tools |
| >=0.6.1 | enum-tools |
| >=3.0.2 | matplotlib |
| >=1.5.0 | netcdf4 |
| >=1.16.2 | numpy |
| >=2.6.2 | openpyxl |
| >=1.0.0 | pandas |
| >=2.2.1 | pymzml |
| >=1.2.1 | scipy |
| >=0.3.0 | sdjson |
| >=3.7.4.3 | typing-extensions |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6.1 | Python |
نحوه نصب
نصب پکیج whl PyMassSpec-2.3.0:
pip install PyMassSpec-2.3.0.whl
نصب پکیج tar.gz PyMassSpec-2.3.0:
pip install PyMassSpec-2.3.0.tar.gz