import networkx as nx
import pandas as pd
from .database import Annotatable
from .transcriptomics import Expression
[docs]class Protein(Expression, Annotatable):
def __init__(self, data, transpose, gene_index=None, usecols=None, gene_level=None, sample_level="sample_index",
transform_fn=None, dropna=False, npartitions=None, cohort_name=None):
"""
Args:
data:
transpose:
gene_index:
usecols:
gene_level:
sample_level:
transform_fn:
dropna:
npartitions:
cohort_name:
"""
super(Protein, self).__init__(data=data, transpose=transpose, gene_index=gene_index, usecols=usecols,
gene_level=gene_level, sample_level=sample_level, transform_fn=transform_fn,
dropna=dropna, npartitions=npartitions, cohort_name=cohort_name)
[docs] @classmethod
def name(cls):
return cls.__name__
[docs] def process_HPRD_PPI_network(self, ppi_data_file_path):
"""
Args:
ppi_data_file_path:
"""
HPRD_PPI = pd.read_table(ppi_data_file_path, header=None)
self.HPRD_PPI_network = nx.from_pandas_edgelist(HPRD_PPI, source=0, target=3,
create_using=nx.DiGraph())