annotate editDB.py @ 2:21ae0e340d80 draft default tip

planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc

# Remove duplicate terms. As well as add any that is needed.

import explodeJSON as ej
from explodeJSON import save_dict_to_json


### create new key
def add_new_key(db, add_key=[]):
    """Set of keys to add to the database"""
    for new_key in add_key:
        db[new_key] = []

    return db


### Add values to dbase:
def add_value_to_term(index_val, db, add_value=[]):
    """index value, put in value"""
    for val in add_value:
        db[index_val].append(val)

    return db


### Remove values from dbase:
def remove_value_from_term(index_val, db, remove_value=[]):
    """remove values from list"""
    for val in remove_value:
        db[index_val].remove(val)

    return db


### Terms to add from a file
def add_from_file(input_file, index_val, db, sep="\n"):
    """input file, new line separated currently, and append files to correct key, return is altered dictionary"""
    terms = open(input_file).read().splitlines()
    db = add_value_to_term(index_val, db, terms)
    return db


if __name__ == "__main__":

    lysis_json = "data/lysis-family-v1.0.2.json"  # insert json of choice
    db = ej.explodeJSON(lysis_json)
    db = db.readJSON()
    # revise_db = add_new_key(db=db,add_key=["spanins"])
    # files = ["data/term_additions/200505_holin_domains.txt","data/term_additions/200505_Spanin_Domains.txt"]
    terms = [
        "DUF2570",
        "PF10828",
        "IPR022538",
        "DUF2514",
        "PF10721",
        "IPR019659",
        "DUF2681",
        "PF10883",
        "IPR020274",
    ]
    # revise_db = add_from_file(files[0],"holin_domains",revise_db)
    # revise_db = add_from_file(files[1],"spanin_domains",revise_db)
    revise_db = add_value_to_term("spanin_domains", db, add_value=terms)
    save_dict_to_json(obj=revise_db, filename="data/lysis-family-v1.0.3.json")