Export Files for GNPS
=====================

With pyOpenMS you can automatically generate all files needed for GNPS Feature-Based Molecular Networking (FBMN) and
Ion Identity Molecular Networking (IIMN).

Pre-requisites are your input :term:`mzML` files and a :py:class:`~.ConsensusMap`, generated by an
`untargeted metabolomics pre-processing workflow <untargeted_metabolomics_preprocessing.html>`_. 
Ensure that :term:`MS2` data has been mapped to the :py:class:`~.FeatureMap` objects with :py:class:`~.IDMapper`.
For IIMN adduct detection must have been performed on the :py:class:`~.FeatureMap` 
objects during pre-processing with :py:class:`~.MetaboliteFeatureDeconvolution`.

First, download two example :term:`mzML` files that have been map aligned based on a :term:`feature map` alignment.

.. code-block:: python

    from urllib.request import urlretrieve

    gh = "https://raw.githubusercontent.com/OpenMS/pyopenms-docs/master"
    urlretrieve(
        gh + "/src/data/Metabolomics_1_aligned.mzML", "Metabolomics_1_aligned.mzML"
    )
    urlretrieve(
        gh + "/src/data/Metabolomics_2_aligned.mzML", "Metabolomics_2_aligned.mzML"
    )
    urlretrieve(
        gh + "/src/data/UntargetedMetabolomics.consensusXML",
        "UntargetedMetabolomics.consensusXML",
    )


.. code-block:: python

    import pyopenms as oms

    mzML_files = ["Metabolomics_1_aligned.mzML", "Metabolomics_2_aligned.mzML"]

    consensusXML_file = "UntargetedMetabolomics.consensusXML"

Since GNPS only works with features that contain :term:`MS2` fragmentation spectra, the first step is to filter out features
from your :py:class:`~.ConsensusMap` that have no :term:`MS2` spectra annotated.

.. code-block:: python

    consensus_map = oms.ConsensusMap()
    oms.ConsensusXMLFile().load(consensusXML_file, consensus_map)
    filtered_map = oms.ConsensusMap(consensus_map)
    filtered_map.clear(False)
    for feature in consensus_map:
        if feature.getPeptideIdentifications():
            filtered_map.push_back(feature)

    consensusXML_file = "filtered.consensusXML"
    oms.ConsensusXMLFile().store(consensusXML_file, filtered_map)

Now you can export your all files for FBMN and IIMN.

.. code-block:: python

    # for FFBM
    oms.GNPSMGFFile().store(
        oms.String(consensusXML_file),
        [file.encode() for file in mzML_files],
        oms.String("MS2data.mgf"),
    )
    oms.GNPSQuantificationFile().store(consensus_map, "FeatureQuantificationTable.txt")
    oms.GNPSMetaValueFile().store(consensus_map, "MetaValueTable.tsv")

    # for IIMN
    oms.IonIdentityMolecularNetworking().annotateConsensusMap(consensus_map)
    oms.IonIdentityMolecularNetworking().writeSupplementaryPairTable(
        consensus_map, "SupplementaryPairTable.csv"
    )