import csv
import logging
from .processor import PhosphoElmProcessor
logger = logging.getLogger(__name__)
[docs]def process_from_dump(fname, delimiter='\t'):
"""Process a Phospho.ELM file dump
The dump can be obtained at http://phospho.elm.eu.org/dataset.html.
Parameters
----------
fname : str
File path to the phospho.ELM file dump.
delimiter : str
The delimiter to use for csv.reader
Returns
-------
indra.sources.phosphoelm.PhosphoElmProcessor
An instance of a PhosphoElmProcessor containing the statements
generated from the file dump
"""
with open(fname, 'r') as f:
csv_reader = csv.reader(f, delimiter=delimiter)
ppelm_json = _get_json_from_entry_rows(csv_reader)
pep = PhosphoElmProcessor(ppelm_json)
pep.process_phosphorylations()
return pep
def _get_json_from_entry_rows(row_iter):
"""Loop body to generate a json friendly structure"""
ppelm_json = []
columns = next(row_iter)
for entry in row_iter:
row_dict = {c: e for c, e in zip(columns, entry)}
ppelm_json.append(row_dict)
return ppelm_json