Interactome

Usage: DBRetina interactome [OPTIONS]

  Construct a features-interactome.

  Detailed description:

  For a groups pairwise file, construct an interactome between the features of
  each group and all other features in the pairwise file.

Options:
  -i, --index-prefix TEXT   index file prefix  [required]
  -p, --pairwise PATH       pairwise TSV file  [required]
  --graphml                 export interactome as graphml file
  --gexf                    export interactome as gexf file
  -o, --output-prefix TEXT  output file prefix  [required]
  --help                    Show this message and exit.

Command arguments

-i, --index-prefix TEXT Index file prefix [required]

This is the user-defined prefix that was used in the indexing step as an output prefix.

-p, --pairwise PATH the pairwise TSV file [required]

The original or a filtered pairwise TSV file.

--graphml

Export interactome as graphml file.

--gexf

Export interactome as gexf file.

-o, --output TEXT output prefix [required]

The output files prefix.

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Output files format

{output_prefix}_interactome.tsv

A pairwise TSV file with the interactome connections.

{output_prefix}_interactome.garphml

An interactome graph in graphml format.

{output_prefix}_interactome.gexf

An interactome graph in gexf format.

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Last update: July 8, 2023
Created: July 8, 2023

Authors: mr-eyes