genesis/fileOps.py at master · batuhand/genesis · GitHub

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from inputClass import Input


class Send:
    def __init__(self,name, site, values, output):
        self.name = name
        self.site = site
        self.values = values


def read_input():
    sendValues = Input()
    f = open("input.txt", "r")
    file = f.readlines()
    for i in file:
        values = i.split(":")
        print(values)
        if values[0] == "transcript":
            sendValues.transcript = values[1]

        elif values[0] == "to":
            site = values[1]

        elif values[0] == "name":
            name = values[1]

        elif values[0] == "snippets refers to":
            sendValues.snippetsrefers = values[1]

        elif values[0] == "first wild type base":
            sendValues.firstwildtype = values[1]

        elif values[0] == "last wild type base":
            sendValues.lastwildtype = values[1]

        elif values[0] == "protein":
            sendValues.protein = values[1]

        elif values[0] == "position":
            sendValues.position = values[1]

        elif values[0] == "AA1":
            sendValues.aa1 = values[1]

        elif values[0] == "AA2":
            sendValues.aa2 = values[1]

        elif values[0] == "alteration":
            sendValues.alteration = values[1]

        elif values[0] == "name of alteration":
            sendValues.nameofalteration = values[1]

        elif values[0] == "gene":
            sendValues.gene = values[1]

        elif values[0] == "inserted bases":
            sendValues.insertedbase = values[1]

        elif values[0] == "new base":
            sendValues.newbase = values[1]

        #sendValues = Input(transcript,snippetsrefers,firstwildtype,lastwildtype,protein,position,aa1,aa2,alteration,nameofalteration,gene,insertedbase,newbase)
        inputObj = Send(name,site,sendValues)

        # make an input object with values

        #elif values[0] == "transcript":
            #values["transcript_stable_id_text"] = values[1]

        print(i)


read_input()


"""
    #---------------- MuTaster
post_values = {"gene": args[0],
                   "transcript_stable_id_text": args[1],
                   "sequence_type": args[2],
                   "sequence_snippet": args[3],
                   "position_be": args[4],
                   "new_base": args[5],
                   "start_insdel": args[6],
                   "end_insdel": args[7],
                   "bases_inserted": args[8]}

                   """


"""------------------ Polyphen

    post_values = {
        "_ggi_project" : "PPHWeb2",
        "_ggi_origin": "query",
        "_ggi_target_submit": "submit",
        "accid" : args[0],
        "seqres": args[1],
        "seqpos" : args[2],
        "seqvar1" : args[3],
        "seqvar2" : args[4],
        #"description":args[5]
    }
    """