Python package for genomic research via biobtree. It aims to provide a strong alternative to similar tools with abilty process large and diverse datasets effectievly and allows executing simple or complex queries between these datasets.
pip install bbpyimport bbpy
import os
# create the package class instance with new or existing folder which data built before.
bb=bbpy.bbpy('specify your directory')
# default database for most studied dataset and organism genomes
# once it is retrieved it is saved to your directory for later reuse
# check document for included dataset or other builtin databases or build custom data
bb.getBuiltInDB()
# starts server for executing queries inside Python pipelines and provide web interface with examples
# web interface address http://localhost:8888/ui/
bb.start()
#Searching identfiers and keywords such as gene name or accessions by passing comma seperated terms.
bb.search('tpi1,vav_mouse,p15498')
#search only within dataset
bb.search("shh,tp53","hgnc")
#Mappings queries allow chains mapping among datasets and in following format
#map(dataset_id).filter(Boolean expression).map(...).filter(...)
# map proteins to go terms
bb.mapping('at5g3_human,vav_human','map(go)',attrs = "type")
# map proteins to go terms types with filter
bb.mapping('at5g3_human,vav_human','map(go).filter(go.type=="biological_process")',attrs = "type")
# stop local server. server can be start again with existing data
bb.stop()