recipe-cluster 0.0.6

Steps for running ReCIPE

Install ReCIPE

pip install recipe-cluster

Download Gene Ontology Data Base

Download gene ontology

Generate DSD file

fastDSD is recommended. It can be used simply by running command:

fastDSD -c --converge -t 0.5 --outfile dscript_distances network-filepath.csv

Generate Cluster File (if necessary)

ReCIPE accepts both CSV and JSON formats for cluster files.

• CSV format: Each line in the CSV represents a cluster of proteins, with each cluster containing a comma-separated list of protein identifiers.

• JSON format: Each key represents a unique cluster ID. The value associated with each key is an object containing a members array, which lists the protein identifiers for that cluster.

Run ReCIPE

Reconnect Clusters

This method analyses cluster, network and DSD files to determine the which proteins qualify to be introduced to clusters in order to create overlapping clusters.

usage: recipe-cluster cook [-h] -cfp CLUSTER_FILEPATH [-cfl CLUSTERS_LABELED] -nfp NETWORK_FILEPATH --outfile OUTFILE [--lb LB] [--ub UB] [--lr LR]
                           [--connectivity-threshold CONNECTIVITY_THRESHOLD] [--metric {degree,components_connected,score}] [--max_proteins MAX_PROTEINS] [--protein_cap PROTEIN_CAP]

options:
  -h, --help            show this help message and exit
  -cfp, --cluster-filepath CLUSTER_FILEPATH
                        Cluster filepath
  -cfl, --clusters-labeled CLUSTERS_LABELED
                        If a CSV file of clusters is passed, clusters have labels. Default: False
  -nfp, --network-filepath NETWORK_FILEPATH
                        Network filepath
  --outfile OUTFILE     Output file to save results
  --lb LB               Lower bound (inclusive) for cluster size. Default: 3
  --ub UB               Upper bound (exclusive) for cluster size. Default: 100
  --lr LR               Linear ratio (if not using sqrt). Default = None
  --connectivity-threshold, -cthresh CONNECTIVITY_THRESHOLD
                        Connectivity threshold to add proteins until. Default = -1.0 (yields connectivity thresholds [0.1, 0.25, 0.5, 0.75, 1.0]) (if only a single option is desired, 0.75
                        is recommended)
  --metric, -wm {degree,components_connected,score}
                        Which metric to use to rank proteins to be added back. Default: degree. Options: degree, components_connected, score
  --max_proteins MAX_PROTEINS
                        Maximises number of proteins to added to a cluster. Default = None
  --protein_cap PROTEIN_CAP
                        Adds at most the number of proteins defined by parameter. Default = 20

In addition to command line access, the cook method can be accessed programmatically with the same arguments as follows:

import recipe-cluster as recipe

recipe.cook(...)