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.

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.

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.