imzml2isa-qt


Nameimzml2isa-qt JSON
Version 0.1.6 PyPI version JSON
download
home_pagehttps://github.com/althonos/imzml2isa-qt
SummaryA PyQt interface for mzml2isa parser.
upload_time2017-01-25 10:34:06
maintainer
docs_urlNone
authorMartin Larralde
requires_python
licenseGPLv3
keywords metabolomics
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
Coveralis test coverage No Coveralis.
            imzml2isa-qt
============

A PyQt interface for mzml2isa parser - imzML edition.
''''''''''''''''''''''''''''''''''''''''''''''''''''''

Overview
--------

This program is a Graphical User Interface for the
`mzml2isa <https://github.com/ISA-tools/mzml2isa>`__ parser. It provides
an easy-to-use interface to convert mzML files to an ISA-Tab Study. It
was made with Python3 and PyQt5.

Install
-------

With PIP
~~~~~~~~

If ``pip`` is present on your system (comes along most of Python install
/ releases), it can be used to install the program and its dependencies:

.. code:: bash

    pip3 install imzml2isa-qt

Without PIP
~~~~~~~~~~~

Once dependencies installed, clone the **imzml2isa-qt** repository to a
folder with writing permissions:

.. code:: bash

    git clone git://github.com/althonos/imzml2isa-qt

After that, either run the GUI directly:

.. code:: bash

    python3 run.py

Or install it locally to run with ``imzmlisa-qt`` command:

.. code:: bash

    cd imzml2isa-qt && python3 setup.py install

Use
---

Open the GUI with the ``imzml2isa-qt`` command. To simply parse **.imzML**
files to **ISA**, select the directory containing your files. With
default settings, the program will create the new ISA files in that
folder, assuming the folder's name is the study identifier (*MTBSLxxx*
for instance for MetaboLights studies). This can be changed by unticking
the ``Export result to directory of each study`` box. Once parameters
are set up, click the ``Convert`` button to start the parser.

MetaboLights
------------

Generating a study to upload on MetaboLights requires pieces of
information the parser cannot guess from the mzML file alone. To provide
more metadata to your final ISA-Tab files, use the ``Add Metadata``
button to open a new window and update details about your study. Still,
even with all the required fields filled, **the generated ISA needs to
be enhanced after the end of the parsing** (using for instance
`Metabolight pre-packaged ISA
Creator <http://www.ebi.ac.uk/metabolights/>`__ to add missing fields).

Missing information required for MetaboLights upload are at the moment:
- Study Factors (sample dependent, must be added to the *study* file
  and to the *investigation* file)
- Metabolite Assignment Files
- Study Designs

TODO
----

-  Either add a ``metabolite assignment file`` field to main window or
   change the **mzml2isa** parser behaviour so that it successfully
   detects metabolite assignment files and add them to the study file.

License
-------

GPLv3

            

Raw data

            {
    "maintainer": "", 
    "docs_url": null, 
    "requires_python": "", 
    "maintainer_email": "", 
    "cheesecake_code_kwalitee_id": null, 
    "keywords": "Metabolomics", 
    "upload_time": "2017-01-25 10:34:06", 
    "author": "Martin Larralde", 
    "home_page": "https://github.com/althonos/imzml2isa-qt", 
    "github_user": "althonos", 
    "download_url": "https://pypi.python.org/packages/be/b1/306345dde5e560e5c0cc2171d220327fd85ce326119b3a6364278ae5e74e/imzml2isa-qt-0.1.6.tar.gz", 
    "platform": "", 
    "version": "0.1.6", 
    "cheesecake_documentation_id": null, 
    "description": "imzml2isa-qt\n============\n\nA PyQt interface for mzml2isa parser - imzML edition.\n''''''''''''''''''''''''''''''''''''''''''''''''''''''\n\nOverview\n--------\n\nThis program is a Graphical User Interface for the\n`mzml2isa <https://github.com/ISA-tools/mzml2isa>`__ parser. It provides\nan easy-to-use interface to convert mzML files to an ISA-Tab Study. It\nwas made with Python3 and PyQt5.\n\nInstall\n-------\n\nWith PIP\n~~~~~~~~\n\nIf ``pip`` is present on your system (comes along most of Python install\n/ releases), it can be used to install the program and its dependencies:\n\n.. code:: bash\n\n    pip3 install imzml2isa-qt\n\nWithout PIP\n~~~~~~~~~~~\n\nOnce dependencies installed, clone the **imzml2isa-qt** repository to a\nfolder with writing permissions:\n\n.. code:: bash\n\n    git clone git://github.com/althonos/imzml2isa-qt\n\nAfter that, either run the GUI directly:\n\n.. code:: bash\n\n    python3 run.py\n\nOr install it locally to run with ``imzmlisa-qt`` command:\n\n.. code:: bash\n\n    cd imzml2isa-qt && python3 setup.py install\n\nUse\n---\n\nOpen the GUI with the ``imzml2isa-qt`` command. To simply parse **.imzML**\nfiles to **ISA**, select the directory containing your files. With\ndefault settings, the program will create the new ISA files in that\nfolder, assuming the folder's name is the study identifier (*MTBSLxxx*\nfor instance for MetaboLights studies). This can be changed by unticking\nthe ``Export result to directory of each study`` box. Once parameters\nare set up, click the ``Convert`` button to start the parser.\n\nMetaboLights\n------------\n\nGenerating a study to upload on MetaboLights requires pieces of\ninformation the parser cannot guess from the mzML file alone. To provide\nmore metadata to your final ISA-Tab files, use the ``Add Metadata``\nbutton to open a new window and update details about your study. Still,\neven with all the required fields filled, **the generated ISA needs to\nbe enhanced after the end of the parsing** (using for instance\n`Metabolight pre-packaged ISA\nCreator <http://www.ebi.ac.uk/metabolights/>`__ to add missing fields).\n\nMissing information required for MetaboLights upload are at the moment:\n- Study Factors (sample dependent, must be added to the *study* file\n  and to the *investigation* file)\n- Metabolite Assignment Files\n- Study Designs\n\nTODO\n----\n\n-  Either add a ``metabolite assignment file`` field to main window or\n   change the **mzml2isa** parser behaviour so that it successfully\n   detects metabolite assignment files and add them to the study file.\n\nLicense\n-------\n\nGPLv3\n", 
    "lcname": "imzml2isa-qt", 
    "bugtrack_url": null, 
    "github": true, 
    "name": "imzml2isa-qt", 
    "license": "GPLv3", 
    "github_project": "imzml2isa-qt", 
    "summary": "A PyQt interface for mzml2isa parser.", 
    "split_keywords": [
        "metabolomics"
    ], 
    "author_email": "martin.larralde@ens-cachan.fr", 
    "urls": [
        {
            "has_sig": false, 
            "upload_time": "2017-01-25T10:34:06", 
            "comment_text": "", 
            "python_version": "source", 
            "url": "https://pypi.python.org/packages/be/b1/306345dde5e560e5c0cc2171d220327fd85ce326119b3a6364278ae5e74e/imzml2isa-qt-0.1.6.tar.gz", 
            "md5_digest": "f0dd477d4d16206e87c769f00b35d668", 
            "downloads": 0, 
            "filename": "imzml2isa-qt-0.1.6.tar.gz", 
            "packagetype": "sdist", 
            "path": "be/b1/306345dde5e560e5c0cc2171d220327fd85ce326119b3a6364278ae5e74e/imzml2isa-qt-0.1.6.tar.gz", 
            "size": 615539
        }, 
        {
            "has_sig": false, 
            "upload_time": "2017-01-25T10:34:14", 
            "comment_text": "", 
            "python_version": "3.6", 
            "url": "https://pypi.python.org/packages/66/e9/97ca779fb6bf6113a24d7ed02cc9210d236e48423f5add5667a30afb76d1/imzml2isa_qt-0.1.6-py3-none-any.whl", 
            "md5_digest": "f087a94caa4581a531fcb7dc0c2e9a5a", 
            "downloads": 0, 
            "filename": "imzml2isa_qt-0.1.6-py3-none-any.whl", 
            "packagetype": "bdist_wheel", 
            "path": "66/e9/97ca779fb6bf6113a24d7ed02cc9210d236e48423f5add5667a30afb76d1/imzml2isa_qt-0.1.6-py3-none-any.whl", 
            "size": 663357
        }
    ], 
    "error": "Could not fetch GitHub repository", 
    "_id": null, 
    "cheesecake_installability_id": null
}