DegRepHunter/ecoparser.py at master · DarkAndroid/DegRepHunter · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
#coding=utf8

import time
import timeit
import os
import sqlite3


# Зверь A T G C GenomeLength GenerationLength TotalLengthOfAllDirectRepeatsReal TotalLengthOfAllDirectRepeatsPseudo001 TotalLengthOfAllDirectRepeatsPseudo002 ... TotalLengthOfAllDirectRepeatsPseudo100


pgen_path = 'Raw\\MammalsGenomesEcology.txt'
pgen = open(pgen_path, "r")

# Species           Sequence    GenerationLength_d  REP.DirRepLength    GenomeLength    A        T       G   C
# Acinonyx_jubatus   genome            2190              3403              17047      5642    4693    2315    4397


path3=("eco.csv")
reps = open(path3, "w")


string = pgen.readline()

#pr=1
while True:

    string = pgen.readline().strip()

    if string == "":
        break
    strarr= string.split("	")
    name = strarr[0]
    genome = strarr[1]
    generlen= strarr[2]
    dirreplrn=  strarr[3]
    genomelen= strarr[4]
    a= strarr[5]
    t= strarr[6]
    g= strarr[7]
    c= strarr[8]
    print (name,c)
    reps.write("%s;%s;%s;%s;%s;%s;%s\n" % (name,a,t,g,c,genomelen,generlen))

    #pr=pr+1