Usage

This script supports the loading of AP-MS data either in Bioplex format via –edgelist and –baitlist flags, or in CM4AI format via the –cm4ai_table flag.

In a project

To use cellmaps_ppidownloader in a project:

import cellmaps_ppidownloader

On the command line

For information invoke cellmaps_ppidownloadercmd.py -h

Usage

cellmaps_ppidownloadercmd.py OUTPUT_DIRECTORY --provenance PROVENANCE_PATH [OPTIONS]

Arguments

• outdir

  The directory where the output will be written to.

Required

• --provenance PROVENANCE_PATH

  Path to file containing provenance information about input files in JSON format. This argument is always required, regardless of which input format you use.

In addition to ``–provenance``, supply either both ``–edgelist`` and ``–baitlist`` or a single ``–cm4ai_table``.

• --edgelist

  APMS edgelist TSV file in the format:

  GeneID1    Symbol1    GeneID2    Symbol2
  10159      ATP6AP2    2          A2M
  

• --baitlist

  APMS baitlist TSV file in the format:

  GeneSymbol    GeneID    # Interactors
  "ADA"         "100"     1
  

• --cm4ai_table

  Path to the CM4AI .tsv file (not just the containing directory) that should contain at least the following columns: Bait, Prey, logOddsScore, FoldChange.x, and BFDR.x.

Optional

• --edgelist_geneid_one_col

  Specifies the name of the column containing the ensemble Gene ID 1 in the –edgelist file. Default is GeneID1.

• --edgelist_symbol_one_col

  Specifies the name of the column containing Gene Symbol 1 in the –edgelist file. Default is Symbol1.

• --edgelist_geneid_two_col

  Specifies the name of the column containing the ensemble Gene ID 2 in the –edgelist file. Default is GeneID2.

• --edgelist_symbol_two_col

  Specifies the name of the column containing Gene Symbol 2 in the –edgelist file. Default is Symbol2.

• --baitlist_symbol_col

  Specifies the name of the column containing the Gene Symbol in the –baitlist file. Default is GeneSymbol.

• --baitlist_geneid_col

  Specifies the name of the column containing the ensemble Gene ID in the –baitlist file. Default is GeneID.

• --baitlist_numinteractors_col

  Specifies the name of the column containing the number of interactors in the –baitlist file. Default is # Interactors.

• --logconf

  Path to the python logging configuration file.

• --skip_logging

  If set, certain log files will not be created.

• --verbose or -v

  Increases the verbosity of the logger to standard error for log messages in this module. This flag stacks, so each additional -v raises verbosity one level. By default (no -v) the tool logs at ERROR level. The mapping is:

  (no -v) = ERROR
  -v      = WARNING
  -vv     = INFO
  -vvv    = DEBUG
  -vvvv   = NOTSET
  

• --version

  Displays the version of the cellmaps_ppidownloader program.

Example usage

The example file can be downloaded from cm4ai.org <https://cm4ai.org>. Go to Products -> Data, log in, and download file for AP-MS with the desired treatment, then unpack the tar gz (tar -xzvf filename.tar.gz).

cellmaps_ppidownloadercmd.py ./cellmaps_ppidownloader_outdir  --cm4ai_table path/to/downloaded/unpacked/dir/apms.tsv --provenance examples/provenance.json

Alternatively, use the files in the example directory in the repository:

1. bait list file: TSV file of baits used for AP-MS experiments

2. edge list file: TSV file of edges for protein interaction network

3. provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)

cellmaps_ppidownloadercmd.py ./cellmaps_ppidownloader_outdir --edgelist examples/edgelist.tsv --baitlist examples/baitlist.tsv --provenance examples/provenance.json

Via Docker

Example usage

Coming soon...