lifs-tools / pymzTab-m

The Python3 language bindings for mzTab-M

Python3 implementation for mzTab-M

This is the mzTab-M reference implementation and validation API service for Python 3.

NOTE: This is an early development version, please use at your own risk and report issues to help improve it!

mzTab-M is intended as a reporting standard for quantitative results from metabolomics/lipodomics approaches. This format is further intended to provide local LIMS systems as well as MS metabolomics repositories a simple way to share and combine basic information.

mzTab-M has been developed with a view to support the following general tasks:

1. Facilitate the sharing of final experimental results, especially with researchers outside the field of metabolomics.
2. Export of results to external software, including programs such as Microsoft Excel® and Open Office Spreadsheet and statistical software / coding languages such as R.
3. Act as an output format of (web-) services that report MS-based results and thus can produce standardized result pages.
4. Be able to link to the external experimental evidence e.g. by referencing back to mzML files.

Related Projects

• mzTab-M 2.0 Standard Specification
• jmzTab-M Reference Implementation and Validator
• jmzTab-M Webapplication and Validator

Overview

This API client was generated by the swagger-codegen project. By using the OpenAPI/Swagger spec from a remote server, you can easily generate an API client.

• API version: 2.0.0
• Package version: 1.0.0

Installation

The pymztab_m package is currently available from Test PyPi.

To install it, run

pip install -i https://test.pypi.org/simple/ pymztab-m-IaaIaaSPDR

This will install the package into your user site-packages directory.

To import it, you can import the following two modules:

• mztab_m_io - Parser implementation for mzTab-M tab separated clear text format.
• mztab_m_swagger_client - Domain model and REST Api to use the mzTab-M validator webapplication

Please have a look at the unit tests (tests directory) for some examples!

Building the Package from Source

Prerequisites

The pymzTab-m package uses pipenv to create an isolated and defined build environment. You will need Python >=3.5 to build the package.

pip3 install pipenv
pipenv install

Activate the pipenv:

pipenv shell

or use

pipenv run

to run commands inside the project directory.

Running the tests

To run the package tests, change into the pipenv and run pytest:

pytest

Alternatively, you can use the setup.py script:

python3 setup.py test

Preparing a distribution

Check that setuptools and wheel are installed and up to date:

python3 -m pip install --upgrade setuptools wheel

Build the distribution package:

python3 setup.py sdist bdist_wheel

Building the documentation

The documentation is built using Sphinx. If not installed, you can install it and a default theme with:

pip3 install sphinx sphinx_rtd_theme

Then change to the docs folder and run:

make html

in order to create the html documentation.