multi_bioservices 3.1.2

This is a multithreaded version of various BioServices functions

Multi Bioservices

Description

multi_bioservices is a utility package for COMO. Its purpose is to provie better multithreaded access to the Bioservices package. This is done by using ThreadPoolExecutors on the synchronous functions. Currently, the only function this package provides is a wrapper around the db2db function in Bioservices.

Installation

To install multi_bioservices, you can use pip:

pip install multi_bioservices

Usage

To use multi_bioservices, simply import the db2db function and call it with the relevant parameters

from multi_bioservices.biodbnet import db2db, InputDatabase, OutputDatabase, TaxonID

db2db(
    input_values=["1", "2", "3"],
    input_db=InputDatabase.GENE_ID,
    output_db=OutputDatabase.GENE_SYMBOL,
    taxon_id=TaxonID.HOMO_SAPIENS
)

Parameters

Parameter	Type	Required?	Default Value	Description
input_values	list[str]	Yes	N/A	The input values to convert
input_db	InputDatabase	Yes	N/A	The input type
output_db	OutputDatabase or list[OutputDatabase]	No	tuple(OutputDatabase.GENE_SYMBOL.value,OutputDatabase.GENE_ID.value, OutputDatabase.CHROMOSOMAL_LOCATION.value	The type to return
taxon_id	TaxonID or int	No	TaxonID.HOMO_SAPIENS (9606)	The taxonomy of the input type
quiet	bool	No	False	Should all output be suppressed?
remove_duplicates	bool	No	False	Should duplicates be removed from the returned dataframe?
cache	bool	No	True	Should cache be used?
delay	int	No	5	How long of a delay should be enforced if the API is accessed to quickly?
concurrency	int	No	8 (max 20)	How many concurrent requests can be made at once?
batch_length	int	No	300 (max 500 if taxon_id is TaxonID.HOMO_SAPIENS)	How many items should be converted at once?

Returns

multi_bioservices returns a dataframe with the input and output databases as column names. The index of the dataframe has been reset, starting at 0

An example dataframe is seen below

Index	Gene ID	Gene Symbol
0	0	-
1	1	A1BG
2	2	A2M
3	3	A2MP1
4	4	-