Retrieve

Retrieves whole proteomes from Uniprot, based in the coast search results. User can provide filtering and ordering settings to define the amount and kind of organisms retrieved.

usage: coast retrieve [-h] [-o OUT] [-max MAX_RETURNS] [-taai MINIMUM_TAAI]
                      [-aai MINIMUM_AAI] [-s {taai,aai,hitspp,match,pmatch}]
                      [-repo REPOSITORY] [-repo_url REPOSITORY_URL]
                      [--verbose] [--id_table]
                      results

Positional Arguments

results

Path to coast search results

Named Arguments

-o, --out

Folder where resulting proteome files will be outputted to.

Default: “/home/docs/checkouts/readthedocs.org/user_builds/coast-tools/checkouts/latest/docs”

-max, --max_returns

The K-top organisms with the best score, defined in sorting parameter. This filtered is applied after all others.

Default: 10

-taai, --minimum_taai

Minimal AAIC threshold for organism selection for proteome retrival.

Default: 0

-aai, --minimum_aai

Minimal AAIBD threshold for organism selection for proteome retrival.

Default: 0

-s, --sorting

Possible choices: taai, aai, hitspp, match, pmatch

Result field used for result sorting, as part of organism selection for retrieval.

Default: “taai”

-repo, --repository

API Endpoint type/format.

Default: “uniprot”

-repo_url, --repository_url

API Endpoint URL for the proteome repository.

Default: “https://www.ebi.ac.uk/proteins/api”

--verbose

Activate verbose terminal output along the created files.

Default: False

--id_table

Save taxid to proteome id correspondence table

Default: False