NSStats - Retrieve basic information about the species and schemas in Chewie-NS
The NSStats module enables the retrieval of information from the Chewie-NS server. Its main objective is to provide information about the list of species and schemas in Chewie-NS, so that users can quickly identify a schema of interest and download it.
Basic Usage
Retrieve the list of species and the total number of schemas, loci and alleles per species:
$ chewBBACA.py NSStats -m species
------------------------------------------------------------------------------
Species id #schemas #loci #alleles
------------------------------------------------------------------------------
Mycobacterium tuberculosis 1 1 2891 748546
Clostridioides difficile 2 1 2147 44556
Salmonella enterica 4 2 11558 7556832
Acinetobacter baumannii 5 1 2390 701466
Arcobacter butzleri 7 4 10592 29956
Campylobacter jejuni 8 1 2794 298415
Escherichia coli 9 1 7601 2958460
Yersinia enterocolitica 10 1 6344 126383
------------------------------------------------------------------------------
Retrieve the list of schemas for a species and the total number of loci and alleles per schema:
$ chewBBACA.py NSStats -m schemas --sp 4
Salmonella enterica (id=4)
------------------------------------------------------------------
Schema_name id #loci #alleles
------------------------------------------------------------------
cgMLSTEnterobase 1 3000 4726816
INNUENDO_cgMLST 2 8558 2830016
------------------------------------------------------------------
Retrieve property values for a schema:
$ chewBBACA.py NSStats -m schemas --sp 4 --sc 2
-------------------------------------
Salmonella enterica - INNUENDO_cgMLST
-------------------------------------
ID: 2
Created by: chewie
Total loci: 8558
Total alleles: 2830016
BLAST Score Ratio: 0.6
chewBBACA version: 2.1.0
Genetic code: 11
Minimum sequence length: 0
Sequence length variation threshold: None
Clustering word size: None
Clustering similarity: None
Representative similarity filter: None
Intracluster similarity filter: None
Creation date: 2020-06-04T23:23:24.099616
Last modified: 2020-06-04T23:23:24.099616
Parameters
-m, --mode (Required) The process can retrieve the list of species ("species"
option) in the Chewie-NS or the list of schemas for a species
("schemas" option).
--sp, --species-id (Optional) The integer identifier of a species in Chewie-NS
(default: None).
--sc, --schema-id (Optional) The integer identifier of a schema in Chewie- NS
(default: None).
--ns, --nomenclature-server (Optional) The base URL for the Chewie-NS instance. The default
value, "main", will establish a connection to "https://chewbbaca.online/",
"tutorial" to "https://tutorial.chewbbaca.online/" and "local" to
"http://127.0.0.1:5000/NS/api/" (localhost). Users may also provide
the IP address to other Chewie-NS instances (default: main).