view tools/myTools/bin/sfa/data/korkut_2015a/__init__.py @ 1:7e5c71b2e71f draft default tip

Uploaded

# -*- coding: utf-8 -*-

"""
[Reference]
Korkut and Wang et al.
Perturbation biology nominates upstream-downstream drug combinations
in RAF inhibitor resistant melanoma cells
eLife (2015) 4:e04640
"""

import os

import numpy as np
import pandas as pd

import sfa
import sfa.base

def create_data():
    dpath = os.path.dirname(__file__)
    fpath_network = os.path.join(dpath, "model_3250.sif")
    return KorkutData("KORKUT_2015A", dpath, fpath_network)


class KorkutData(sfa.base.Data):

    def __init__(self, abbr, dpath, fpath_network):

        self._abbr = abbr
        self._name = "Korkut and Wang et al. eLife 2015;4:e04640"

        fpath_ptb = os.path.join(dpath, "ptb.tsv")

        A, n2i, dg = sfa.read_sif(fpath_network, as_nx=True)
        self._A = A
        self._n2i = n2i
        self._dg = dg
        self._df_conds = pd.read_table(os.path.join(dpath, "conds.tsv"),
                                       header=0, index_col=0)
        self._df_exp = pd.read_table(os.path.join(dpath, "exp.tsv"),
                                     header=0, index_col=0)

        self._inputs = {}
        self._df_ptb = pd.read_table(fpath_ptb, index_col=0)
        if any(self._df_ptb.Type == 'link'):
            self._has_link_perturb = True
        else:
            self._has_link_perturb = False

        
        # Remove the rows and columns of a node which is not
        # included in the given network structure.
        not_included = set(self._df_conds.columns) - set(self._n2i.keys())
        for target in not_included:
            ind_removed = self._df_conds[self.df_conds[target] != 0].index
            self._df_conds.drop(ind_removed, inplace=True)
            self._df_conds.drop([target], axis=1, inplace=True)
            self._df_exp.drop(ind_removed, inplace=True)
            self._df_ptb.drop([target], inplace=True)
            
            # Re-index according to the new size.
            self._df_conds.index = np.arange(1, self._df_exp.shape[0]+1)
            self._df_exp.index = self._df_conds.index


        self._names_ptb = []
        for i, row in enumerate(self._df_conds.iterrows()):
            row = row[1]
            list_name = []  # Target names
            for target in self._df_conds.columns[row.nonzero()]:
                list_name.append(target)
            # end of for
            self._names_ptb.append(list_name)
        # end of for

        s1 = set(self._df_exp.columns)  # From experimental data
        s2 = set(n2i.keys())  # From network
        exp_only = s1 - s2
        self._df_exp.drop(exp_only, axis=1, inplace=True)


        # For mapping from the indices of adj. matrix to those of DataFrame
        # (arrange the indices of adj. matrix according to df_exp.columns)
        self._iadj_to_idf = [n2i[x] for x in self._df_exp.columns]
        self._i2n = {idx: name for name, idx in n2i.items()}
    # end of def __init__