get_proteomes.py

get_proteomes.py implements a method that we apply before finding HGT candidates with ShadowCaster. This script retrieves a list of proteomes from phylogenetically related species to the query species (fasta files) from the NCBI ftp. ShadowCaster needs these proteomes to construct a phylogenetic shadow used in its phylogenetic component.

Prerequisites

  • EDirect UNIX command line of NCBI.

Before using the script, check that the commands esearch and xtract work correctly in a new shell window.

type esearch xtract

Usage

The usage and help documentation of get_proteomes.py can be seen by running python get_proteomes.py -h:

Example

An example of how to run get_proteomes.py on the test data:

cd ShadowCaster/scripts
python get_proteomes.py -n Rhodanobacter_denitrificans -sp 25

This results in the following output files in the folder named with the species name provided:

  • log.txt Name of the downloaded species and its ftp address.
  • proteomes folder Proteomes (fasta file) used to construct the shadow.

The results should be similar to those found in the proteomes-output folder of the test data repository, see here