python计算长度_python计算基因组外显子长度（第一题）

题目来自生信技能树

统计人类外显子长度

坐标的文件可如下下载

import os

import re

from collections import OrderedDict

from operator import itemgetter

os.chdir("D:\python")

ha1 = {}

exonLength = 0

with open("CCDS.current.txt","rt") as f:

for line in f:

if line.startswith("#"):

continue

line = line.rstrip()

lst = line.split('\t')

if lst[-2] == '-':

continue

lst[-2] = re.sub('\[|\]','',lst[-2])

exons = lst[-2].split(", ")

for exon in exons:

start = int(exon.split('-')[0])

end = int(exon.split('-')[1])

coordinate = lst[0] + ':' + exon

if coordinate not in ha1:

ha1[coordinate] = 1

exonLength += end - start

print(exonLength)

419272

ha1 = {}

exonLength = 0

with open("CCDS.current.txt","rt") as f:

for line in f:

if line.startswith("#"):

continue

line = line.rstrip()

lst = line.split('\t')

if lst[-2] == '-':

continue

lst[-2] = re.sub('\[|\]','',lst[-2])

exons = lst[-2].split(", ")

for exon in exons:

start = int(exon.split('-')[0])

end = int(exon.split('-')[1])

for i in range(start,end):

coordinate = lst[0] + ':' + str(i)

if coordinate not in ha1:

exonLength += 1

print(exonLength)

451017