Source code for indra.sources.ubibrowser.api

__all__ = ['process_from_web', 'process_file', 'process_df']

import pandas
from .processor import UbiBrowserProcessor


DOWNLOAD_URL = 'http://ubibrowser.bio-it.cn/ubibrowser_v3/Public/download/literature/'
E3_URL = DOWNLOAD_URL + 'literature.E3.txt'
DUB_URL = DOWNLOAD_URL + 'literature.DUB.txt'


[docs]def process_from_web() -> UbiBrowserProcessor: """Download the UbiBrowser data from the web and process it. Returns ------- : An UbiBrowserProcessor object with INDRA Statements extracted in its statements attribute. """ e3_df = pandas.read_csv(E3_URL, sep='\t') dub_df = pandas.read_csv(DUB_URL, sep='\t') return process_df(e3_df, dub_df)
[docs]def process_file(e3_path: str, dub_path: str) -> UbiBrowserProcessor: """Process UbiBrowser data from files. Parameters ---------- e3_path : The path to the E3 file. dub_path : The path to the DUB file. Returns ------- : An UbiBrowserProcessor object with INDRA Statements extracted in its statements attribute. """ e3_df = pandas.read_csv(e3_path, sep='\t') dub_df = pandas.read_csv(dub_path, sep='\t') return process_df(e3_df, dub_df)
[docs]def process_df(e3_df: pandas.DataFrame, dub_df: pandas.DataFrame) \ -> UbiBrowserProcessor: """Process data frames containing UbiBrowser data. Parameters ---------- e3_df : A data frame containing UbiBrowser E3 data. dub_df : A data frame containing UbiBrowser DUB data. Returns ------- : An UbiBrowserProcessor object with INDRA Statements extracted in its statements attribute. """ up = UbiBrowserProcessor(e3_df, dub_df) up.extract_statements() return up