Reference Manual¶

module PseudomonasDotComScraper:
	Hosting the PseudomonasDotComScraper, an API for the https://www.pseudomonas.com database web interface.

class GenDBScraper.PseudomonasDotComScraper.PseudomonasDotComScraper(query=None)[source]¶

An API for the pseudomonas.com genome database using web scraping technology.

from_json(infile)[source]¶

Deserialize a json file into a results dictionary (a dict of pandas.DataFrame).

Parameters:	infile (str) – The file path of the json file to load.

query¶

Get the query.

Returns:	The query object.
Return type:	pdc_query

run_query(query=None)[source]¶

Run a query on pseudomonas.com

Parameters:	query ([list of] (pdc_query \| dict)) – The query object to run.
Returns:	The query results as a dictionary with ‘strain_feature’ keys.
Return type:	dict

to_json(results, outfile=None)[source]¶

Serialize results dictionary to json.

Parameters:	results (dict) – The results dictionary (dict of pandas.DataFrame). outfile (str) – Path to file for writing query results to. Default: None, will write to temp file.
Raises:	IOError – ‘outfile’ not writable.
Returns:	If successful, path to written file.

class GenDBScraper.PseudomonasDotComScraper.pdc_query(strain, feature, organism)¶