biobtreePy

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.

Installation

pip install bbpy

Usage

import 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()