Source code for bionetgen.atomizer.biogrid

# -*- coding: utf-8 -*-
"""
Created on Tue Nov 12 13:44:53 2013

@author: proto
"""

import csv

try:
    import pandas as pd
except ImportError:
    pd = None


def loadBioGrid(fileName="BIOGRID-ALL-3.2.108.tab2.txt"):
    if hasattr(loadBioGrid, "db"):
        return loadBioGrid.db
    loadBioGrid.db = {}

    def check(db, term):
        if term not in db:
            db[term] = set([])

    f = open(fileName, "rb")
    content = csv.DictReader(f, delimiter="\t")
    loadBioGrid.db["synonyms"] = {}

    for idx, line in enumerate(content):
        tmp = {}
        tmp["osiB"] = line["Official Symbol Interactor B"]
        tmp["osiA"] = line["Official Symbol Interactor A"]
        tmp["siA"] = line["Synonyms Interactor A"].split("|")
        tmp["siB"] = line["Synonyms Interactor B"].split("|")

        tmp["siA"].append(tmp["osiA"])
        tmp["siB"].append(tmp["osiB"])
        comb = ([x, y] for x in tmp["siA"] for y in tmp["siB"])

        """
        for element in tmp['siA']:
            check(loadBioGrid.db['synonyms'], element.upper())
            loadBioGrid.db['synonyms'][element.upper()] = tmp['osiA'].upper()
        for element in tmp['siB']:
            check(loadBioGrid.db['synonyms'], element.upper())
            loadBioGrid.db['synonyms'][element.upper()] = tmp['osiB'].upper()
        if tmp['osiA'].upper() in loadBioGrid.db['synonyms']:
            tmp['osiA'] = loadBioGrid.db['synonyms'][tmp['osiA'].upper()]
        if tmp['osiB'].upper() in loadBioGrid.db['synonyms']:
            tmp['osiB'] = loadBioGrid.db['synonyms'][tmp['osiB'].upper()]
        """

        for element in comb:
            check(loadBioGrid.db, element[1].upper())
            loadBioGrid.db[element[1].upper()].add(element[0].upper())

        # check(loadBioGrid.db, tmp['osiA'].upper())
        # loadBioGrid.db[tmp['osiA'].upper()].add(tmp['osiB'].upper())
    p = pd.Series(loadBioGrid.db)
    p.to_hdf("BioGridPandas.h5", "biogrid")


def loadBioGridDict(fileName="BioGridPandas.h5"):
    if hasattr(loadBioGrid, "db"):
        return loadBioGrid.db
    if pd is None:
        print("pandas library not found.")
        loadBioGrid.db = {}
    else:
        try:
            loadBioGrid.db = pd.read_hdf(fileName, "biogrid")
        except:
            print("Biogrid database not found")
            loadBioGrid.db = {}

    return loadBioGrid.db


if __name__ == "__main__":
    # extractStatistics()
    db = loadBioGrid()
    # print len(db)
    # f = open('bioGridDict.dump', 'wb')
    # pickle.dump(db, f)
    # pass
    # db2 = loadBioGridDict()
    # print len(db2)
    # f = open('bioGridDict.dump', 'wb')
    # print len(db)
    # loadBioGrid()
    # print len(db2)