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.
To install multi_bioservices, you can use pip:
pip install multi_bioservicesTo 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
)| 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? |
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 | - |
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