nmrml2isa
=========
|Version| |Py versions| |Git| |Build Status| |License| |RTD doc| |DOI|
|NMRML|
Overview
--------
nmrml2isa is a Python3 program that can be used to generate an ISA-Tab structured
investigation out of nmrML files, providing the backbone of a study that can then be
edited with an ISA editing tool (see `MetaboLights pre-packaged
ISA Creator <http://www.ebi.ac.uk/metabolights/>`__)
Install
-------
See the `Installation page <http://2isa.readthedocs.io/en/latest/nmrml2isa/install.html>`__ of
the `online documentation <http://2isa.readthedocs.io/en/latest/nmrml2isa/index.html>`__.
Use
---
See the `Usage page <http://2isa.readthedocs.io/en/latest/nmrml2isa/usage.html>`__ and
the `Examples page <http://2isa.readthedocs.io/en/latest/nmrml2isa/examples.html>`__ for
more detailed descriptions of usage and examples.
CLI
~~~
The parser comes with a simple one-liner:
.. code:: bash
mzml2isa -i /path/to/nmrml_files/ -o /path/to/out_folder -s name_of_study
Module
~~~~~~
It possible to import **nmrml2isa** as a Python module:
.. code:: python
from nmrml2isa import parsing
in_dir = "/path/to/nmrml_files/"
out_dir = "/path/to/out_folder/"
study_identifier_name = "name_of_study"
parsing.full_parse(in_dir, out_dir, study_identifier_name)
Meta extraction
~~~~~~~~~~~~~~~~
If you just want to extract the meta information without writing them
in ISA-Tab files, it is possible to do so either by running the ``nmrml2isa.nmrml``
module as main:
.. code:: bash
python -m nmrml2isa.nmrml /path/to/your/file.nmrML
# this will produce a JSON dict of all extracted metadata
Or within a python program with the **nmrml** submodule:
.. code:: python
from nmrml2isa import nmrml
nmrml_path = "/path/to/file.nmrML"
nmrml_meta = nmrml.nmrMLmeta(nmrml_path)
# python dictionnary
print(nmrml_meta.meta)
# json dictionnary
print(nmrml_meta.meta_json)
.. |Build Status| image:: https://img.shields.io/travis/ISA-tools/nmrml2isa.svg?style=flat&maxAge=2592000
:target: https://travis-ci.org/ISA-tools/nmrml2isa
.. |Py versions| image:: https://img.shields.io/pypi/pyversions/nmrml2isa.svg?style=flat&maxAge=2592000
:target: https://pypi.python.org/pypi/nmrml2isa/
.. |Version| image:: https://img.shields.io/pypi/v/nmrml2isa.svg?style=flat&maxAge=2592000
:target: https://pypi.python.org/pypi/nmrml2isa/
.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=2592000
:target: https://github.com/ISA-tools/nmrml2isa
.. |License| image:: https://img.shields.io/pypi/l/nmrml2isa.svg?style=flat&maxAge=2592000
:target: https://www.gnu.org/licenses/gpl-3.0.html
.. |RTD doc| image:: https://img.shields.io/badge/documentation-RTD-71B360.svg?style=flat&maxAge=2592000
:target: http://2isa.readthedocs.io/en/latest/nmrml2isa/index.html
.. |DOI| image:: https://zenodo.org/badge/74688415.svg
:target: https://zenodo.org/badge/latestdoi/74688415
.. |NMRML| image:: http://nmrml.org/images/header-mark.jpg
:target: http://nmrml.org/
Raw data
{
"_id": null,
"home_page": "http://github.com/althonos/nmrml2isa",
"name": "nmrml2isa",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "Metabolomics,NMR,Nuclear Magnetic Resonance,ISA Tab,nmrML,metabolites,parsing",
"author": "Martin Larralde",
"author_email": "martin.larralde@ens-cachan.fr",
"download_url": "https://files.pythonhosted.org/packages/c3/fb/c5a9965e80310c086286ef0b94df8c90a55ac5c35b9dde67aadcedefd8bc/nmrml2isa-0.3.3.tar.gz",
"platform": null,
"description": "nmrml2isa\n=========\n|Version| |Py versions| |Git| |Build Status| |License| |RTD doc| |DOI|\n\n|NMRML|\n\nOverview\n--------\n\nnmrml2isa is a Python3 program that can be used to generate an ISA-Tab structured\ninvestigation out of nmrML files, providing the backbone of a study that can then be\nedited with an ISA editing tool (see `MetaboLights pre-packaged\nISA Creator <http://www.ebi.ac.uk/metabolights/>`__)\n\nInstall\n-------\n\nSee the `Installation page <http://2isa.readthedocs.io/en/latest/nmrml2isa/install.html>`__ of\nthe `online documentation <http://2isa.readthedocs.io/en/latest/nmrml2isa/index.html>`__.\n\n\nUse\n---\n\nSee the `Usage page <http://2isa.readthedocs.io/en/latest/nmrml2isa/usage.html>`__ and\nthe `Examples page <http://2isa.readthedocs.io/en/latest/nmrml2isa/examples.html>`__ for\nmore detailed descriptions of usage and examples.\n\nCLI\n~~~\n\nThe parser comes with a simple one-liner:\n\n.. code:: bash\n\n mzml2isa -i /path/to/nmrml_files/ -o /path/to/out_folder -s name_of_study\n\n\nModule\n~~~~~~\n\nIt possible to import **nmrml2isa** as a Python module:\n\n.. code:: python\n\n from nmrml2isa import parsing\n\n in_dir = \"/path/to/nmrml_files/\"\n out_dir = \"/path/to/out_folder/\"\n study_identifier_name = \"name_of_study\"\n\n parsing.full_parse(in_dir, out_dir, study_identifier_name)\n\n\nMeta extraction\n~~~~~~~~~~~~~~~~\n\nIf you just want to extract the meta information without writing them\nin ISA-Tab files, it is possible to do so either by running the ``nmrml2isa.nmrml``\nmodule as main:\n\n.. code:: bash\n\n python -m nmrml2isa.nmrml /path/to/your/file.nmrML\n # this will produce a JSON dict of all extracted metadata\n\n\nOr within a python program with the **nmrml** submodule:\n\n.. code:: python\n\n from nmrml2isa import nmrml\n\n nmrml_path = \"/path/to/file.nmrML\"\n nmrml_meta = nmrml.nmrMLmeta(nmrml_path)\n\n # python dictionnary\n print(nmrml_meta.meta)\n\n # json dictionnary\n print(nmrml_meta.meta_json)\n\n\n\n\n.. |Build Status| image:: https://img.shields.io/travis/ISA-tools/nmrml2isa.svg?style=flat&maxAge=2592000\n :target: https://travis-ci.org/ISA-tools/nmrml2isa\n\n.. |Py versions| image:: https://img.shields.io/pypi/pyversions/nmrml2isa.svg?style=flat&maxAge=2592000\n :target: https://pypi.python.org/pypi/nmrml2isa/\n\n.. |Version| image:: https://img.shields.io/pypi/v/nmrml2isa.svg?style=flat&maxAge=2592000\n :target: https://pypi.python.org/pypi/nmrml2isa/\n\n.. |Git| image:: https://img.shields.io/badge/repository-GitHub-blue.svg?style=flat&maxAge=2592000\n :target: https://github.com/ISA-tools/nmrml2isa\n\n.. |License| image:: https://img.shields.io/pypi/l/nmrml2isa.svg?style=flat&maxAge=2592000\n :target: https://www.gnu.org/licenses/gpl-3.0.html\n\n.. |RTD doc| image:: https://img.shields.io/badge/documentation-RTD-71B360.svg?style=flat&maxAge=2592000\n :target: http://2isa.readthedocs.io/en/latest/nmrml2isa/index.html\n\n.. |DOI| image:: https://zenodo.org/badge/74688415.svg\n :target: https://zenodo.org/badge/latestdoi/74688415\n \n.. |NMRML| image:: http://nmrml.org/images/header-mark.jpg\n :target: http://nmrml.org/\n",
"bugtrack_url": null,
"license": "GPLv3",
"summary": "nmrml2isa - nmrML to ISA-Tab parsing tool",
"version": "0.3.3",
"project_urls": {
"Homepage": "http://github.com/althonos/nmrml2isa"
},
"split_keywords": [
"metabolomics",
"nmr",
"nuclear magnetic resonance",
"isa tab",
"nmrml",
"metabolites",
"parsing"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "5a2debb401671cca8f2ca22fe58c29f6aabe95ad88ed1c165f8a40a292d89f4e",
"md5": "61b304a0cd7ceb3f6d7197c0bb3dd90f",
"sha256": "2d0e8f7f233ffe2d7b2e4444ae6caa9a37b40c689af94b9b97228b862766a0a9"
},
"downloads": -1,
"filename": "nmrml2isa-0.3.3-py3-none-any.whl",
"has_sig": false,
"md5_digest": "61b304a0cd7ceb3f6d7197c0bb3dd90f",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 87446,
"upload_time": "2023-11-06T16:00:55",
"upload_time_iso_8601": "2023-11-06T16:00:55.443832Z",
"url": "https://files.pythonhosted.org/packages/5a/2d/ebb401671cca8f2ca22fe58c29f6aabe95ad88ed1c165f8a40a292d89f4e/nmrml2isa-0.3.3-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "c3fbc5a9965e80310c086286ef0b94df8c90a55ac5c35b9dde67aadcedefd8bc",
"md5": "25c69cb25bd97c7f8b07a9520afd9a31",
"sha256": "87269827b36b7df01f8909e4148c67ad585d8441432135fe41bf8abf4c41e99f"
},
"downloads": -1,
"filename": "nmrml2isa-0.3.3.tar.gz",
"has_sig": false,
"md5_digest": "25c69cb25bd97c7f8b07a9520afd9a31",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 83728,
"upload_time": "2023-11-06T16:00:57",
"upload_time_iso_8601": "2023-11-06T16:00:57.299614Z",
"url": "https://files.pythonhosted.org/packages/c3/fb/c5a9965e80310c086286ef0b94df8c90a55ac5c35b9dde67aadcedefd8bc/nmrml2isa-0.3.3.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-11-06 16:00:57",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "althonos",
"github_project": "nmrml2isa",
"github_not_found": true,
"lcname": "nmrml2isa"
}
JSON
