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https://github.com/Priyatham-sai-chand/compara-deep-learning.git
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57 lines
1.4 KiB
Python
57 lines
1.4 KiB
Python
import sys
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import os
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from req_data import get_data_file,download_data
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from read_data import read_data_genome,read_data_homology
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from process_data import list_dict_genomes,create_chromosome_maps
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def get_data_genome(arg,dir):
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a=[]
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d={}
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ld=[]
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ldg=[]
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if arg[0]=='-d':
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if arg[2]=="-r":
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c=0
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else:
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return a,d,ld,ldg,dict(),dict()
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elif arg[0]=='-f':
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get_data_file(arg[1],dir)
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elif arg[0]=="-nd":
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return ld,ldg,a,d,dict(),dict()
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if arg[2]=="-r":
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a,d=read_data_genome(dir,a,d)
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assert(len(a)==len(d))
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print("Creating Maps:")
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ld,ldg=list_dict_genomes(a,d)
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cmap,cimap=create_chromosome_maps(a,d)
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assert(len(ld)==len(ldg))
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for i in range(len(ld)):
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assert(len(ld[i])==len(ldg[i]))
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return cmap,cimap,ld,ldg,a,d
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def get_data_homology(arg,dir):
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a_h=[]
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d_h={}
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if arg[0]=="-l":
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if not os.path.exists(dir):
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os.mkdir(dir)
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download_data(arg[1],dir)
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elif arg[0]=="-f":
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get_data_file(arg[1],dir)
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elif arg[0]=="-d":
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if arg[2]=="-r":
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c=0
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else:
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return a_h,d_h
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elif arg[2]=="-nd":
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return a_h,d_h
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if arg[2]=="-r":
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a_h,d_h=read_data_homology(dir)
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assert(len(a_h)==len(d_h))
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return a_h,d_h
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