compara-deep-learning/get_data.py

import sys
import os
from req_data import get_data_file,download_data
from read_data import read_data_genome,read_data_homology
from process_data import list_dict_genomes,create_chromosome_maps

def get_data_genome(arg,dir):
    a=[]
    d={}
    ld=[]
    ldg=[]
    if arg[0]=='-d':
        if arg[2]=="-r":
            c=0
        else:
            return a,d,ld,ldg,dict(),dict()
    elif arg[0]=='-f':
        get_data_file(arg[1],dir)
    elif arg[0]=="-nd":
        return ld,ldg,a,d,dict(),dict()

    if arg[2]=="-r":
        a,d=read_data_genome(dir,a,d)
        assert(len(a)==len(d))
        print("Creating Maps:")
        ld,ldg=list_dict_genomes(a,d)
        cmap,cimap=create_chromosome_maps(a,d)

        assert(len(ld)==len(ldg))

        for i in range(len(ld)):
            assert(len(ld[i])==len(ldg[i]))

    return cmap,cimap,ld,ldg,a,d

def get_data_homology(arg,dir):
    a_h=[]
    d_h={}
    if arg[0]=="-l":
        if not os.path.exists(dir):
            os.mkdir(dir)
        download_data(arg[1],dir)
    elif arg[0]=="-f":
        get_data_file(arg[1],dir)
    elif arg[0]=="-d":
        if arg[2]=="-r":
            c=0
        else:
            return a_h,d_h
    elif arg[2]=="-nd":
        return a_h,d_h

    if arg[2]=="-r":
        a_h,d_h=read_data_homology(dir)
        assert(len(a_h)==len(d_h))

    return a_h,d_h