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Outputs
=======

The tool creates several files and folders in the specified output directory.
Below is the list and description of each output generated by the tool.

Output files and directories
-----------------------------

- ``baitlist.tsv``
    This file contains information about the bait proteins used in the affinity purification-mass spectrometry (AP-MS) process.
    (from input, not always generated)

- ``edgelist.tsv``
    An edge list representation of the protein-protein interactions. Each row in this file represents an interaction between two proteins.
    (from input, not always generated)

- ``ppi_edgelist.tsv``
    A processed edge list file which represents protein-protein interactions, where proteins are identified by their symbols.

.. code-block::

    geneA	geneB
    DNMT3A	SAP18
    DNMT3A	DDX3X
    DNMT3A	SEC16A
    DNMT3A	U2SURP
    DNMT3A	SYNJ2

- ``ppi_gene_node_attributes.tsv``
    Contains attributes for each gene node in the protein-protein interaction network. This includes information like gene names, ensembl ID, and other relevant data.

.. code-block::

    name	represents	ambiguous	bait
    DNMT3A	ensembl:ENSG00000119772		TRUE
    HDAC2	ensembl:ENSG00000196591		TRUE
    KDM6A	ensembl:ENSG00000147050		TRUE
    SMARCA4	ensembl:ENSG00000127616		TRUE

Logs and Metadata
-----------------

- ``ppi_gene_node_attributes.errors``
    If there are any errors encountered while processing the gene node attributes, they will be logged in this file.

- ``output.log``
    Log file detailing the operational logs of the script. Useful for understanding the flow of operations and debugging any issues.

- ``error.log``
    Log file specifically capturing any errors encountered during the script's execution.

- ``ro-crate-metadata.json``
    Metadata in RO-Crate format, a community effort to establish a lightweight approach to packaging research data with their metadata.

    The main object contains identifier (@id), type (@type), name, descriptions, keywords and isPartOf, that describes the hierarchical relationship (organization and project).

    Graph: The @graph key contains an array of objects that detail other entities related to the main dataset.
    a. Metadata, Datasets, Software
    b. Output Files: details of output files generated by the tool.