python 根据染色体起始终止点坐标来获取碱基序列

在工作当中，有时候我们知到染色体编号以及染色体起始终止坐标，我们想知道这段序列是什么样的碱基。
其一，我们一般用去UCSC的genome browser里面去查询 ，其实也可以从UCSC的接口去解析网页，然后在提取序列信息
比如chr17:7676091,7676196 ，那么我只需要构造下面一个网页地址 http://genome.ucsc.edu/cgi-bin/das/hg38/dna?segment=chr17:7676091,7676196
然后 hg38可以更换成hg19，dna?segment= 后面可以按照标准格式更换，就可以返回我们想要的序列了。现在对网页返回 一个xml格式的信息，用python解析一下

  1 import requests

import re
from bs4 import BeautifulSoup
import xlwt
import xlrd
from xlutils.copy import copy
import os ,sys
#print(sys.path)
cwd=os.getcwd()



def getHTMLText(url):
    print("111111")
    try:
        header = {'user-agent': 'Mozilla/5.0'}
        r = requests.get(url,headers = header,timeout = 30 )
        r.raise_for_status()
        r.encoding =r.apparent_encoding
        print("get 222222222222222")
        return r.text
    except:
        return ""

def fillDNAList(dnalist, html):
    # 使用正则表达式获取dna 序列的头文件
    match = re.search('SEQUENCE([sS]*?version="1.00")', html)
    print("match ok")
    if match:
        dna_header = re.search('SEQUENCE([sS]*?version="1.00")', html)
        #print('10====>', dna_header.group())
        #dna_header 存到列表
        dnalist.append(dna_header.group())

    match = re.search('DNA.*?length="(d*)"', html)
    if match:
        length_header= re.search('DNA.*?length="(d*)"', html)
        #print('11=====>', length_header.group())
        dnalist.append(length_header.group())

    #使用 BeautifulSoup
    print("BeautifulSoup tag属性 获取dna标签属性的字符串部分")
    soup = BeautifulSoup(html, 'html.parser')
    tag = soup.dna
    seq = soup.dna.string
    seq = seq.replace('
','').upper()  #换行符删除掉,转换成大写
    # seq 存到列表
    dnalist.append(seq)
    print("final======>",dnalist)
    return dnalist

def write_excell(dnalist,chrnum,pos):
    head = '>hg19' + ' ' + dnalist[0] + dnalist[1]
    f = xlwt.Workbook(encoding='utf-8', style_compression=0) #创建新的Excel（新的workbook）
    sheet = f.add_sheet('test8', cell_overwrite_ok=True) #创建新的表单
    # 先写第一行的头文件
    sheet.write(0,0,head)
    #再从第二行开始写，每行写入50 个字符串
    dna = dnalist[2]
    print('=====',dna,type(dna))
    for i in range(0,len(dna),50):
        sheet.write((int((i+1)/50))+1,0,dna[i:i+50])

    out_file = 'chrmosome%s_%s.xls'% (chrnum,pos)
    f.save(out_file)
    out_file_dir = os.path.join(cwd, out_file)
    return out_file_dir

def modify_excell(out_file_dir,chrnum,pos):
    '''
    改Excel表（xlutils模块）
    :return:
    '''
    rb = xlrd.open_workbook(out_file_dir)  # 打开out_file.xls文件,创建工作簿实例对象
    sheet = rb.sheet_by_index(0)
    nrow11 = sheet.cell_value(10, 0) #修改第11行第一列，索引是10，0
    # 根据需要截取原单元格里面的内容与需要添加的内容进行拼接
    new_nrow11 = '[' + nrow11
    # 同理操作nrow12
    nrow12 = sheet.cell_value(11, 0)
    new_nrow12 = nrow12 + ']'

    wb = copy(rb)
    ws = wb.get_sheet(0)
    # 往单元格中写入拼接后的新字符串内容
    ws.write(10,0,new_nrow11)
    ws.write(11, 0, new_nrow12)
    modify_file = 'new_chrmosome%s_%s.xls' % (chrnum,pos)
    wb.save(modify_file)

def main():
    hg19 = "hg19"
    chrnum = 17
    pos = 7676091
    start = pos - 500
    end = pos + 500
    position_DNA_list = []
    url = f"http://genome.ucsc.edu/cgi-bin/das/{hg19}/dna?segment=chr{chrnum}:{start},{end}"
   
    print(url)
    html = getHTMLText(url)
    dnalist = fillDNAList(position_DNA_list,html)
    out_file_dir = write_excell(dnalist,chrnum,pos)
    modify_excell(out_file_dir,chrnum,pos)

main()

结果如下：

http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr17:7675591,7676591

match ok
BeautifulSoup tag属性 获取dna标签属性的字符串部分
final======> ['SEQUENCE id="chr17" start="7675591" stop="7676591" version="1.00"', 'DNA length="1001"', 'CCCAAGAGCCTTCAGTATACACATCAATAAAAATAATTTTAATTATTCTGATAAAAGATAAACATGAAAAGTTATGGTATGCAAAGTTGAATGACAACAACTGATACTATTTGAAATAATTGACAGAATTATATTCCGTAACAATTTATAAGCAAAGCCAAAAAAACAATGATCCCTTTGTTGAATGCACAGAACAAATCCATCTTGTCCACGGCTACTGAGCATGCCTGTGATCTCCAGGGGTCACTCAGGTTTGACTCAAAGGATCCAACAGCCTGTAGACCCTGTGCTTGAAGGCATGAGGGTCACCTCTGAGTTCACACTCACTAGTGTCCCTCCTTTCTTCAGAAAGCTAGGAACTGGGAAGACAAGGGGAAAATCAATCAAGGCCTGAGGTATGGGGCTGTAGGCTGGGAGGAAACTAACATTATTGAGAAGCTACTGATGTGAATACATTTCAATTACTACTCACATTGGTTTTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTTTTAAGACGGAGTTTTGCTCTCGTTGCCCAGGCTGGAGTGCAATGGAATGATCTAAGGTCACCACAACCTCCACCTCCCGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGTGTGCCACCACACCCAGCTAAGTTTGTATTTTTTTAGTAGAGACGGTGTTTCACCATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCAAGTGATCCACCCACCTCGGCCTCCCAAAGTGCTGGGATTATAGGCATGAGCCACCACACCCAGCCTCACGTTGGTTTTTGAGATGGATTTTATTGCCATTTTGTACACAAAAAGGTCAAAACTCAGTGAGGTGAATTGACATGACAGTAAGTGAAAGAACTACTATCTGATTGGGGGTCTTCTGCCGCCTGCTCTGGGACTCTTTCTGCTATGACATGAAGGACATTGGCAACCCCAGTCCTTGCAGATTTCTTTCACTGTGTGC']
===== CCCAAGAGCCTTCAGTATACACATCAATAAAAATAATTTTAATTATTCTGATAAAAGATAAACATGAAAAGTTATGGTATGCAAAGTTGAATGACAACAACTGATACTATTTGAAATAATTGACAGAATTATATTCCGTAACAATTTATAAGCAAAGCCAAAAAAACAATGATCCCTTTGTTGAATGCACAGAACAAATCCATCTTGTCCACGGCTACTGAGCATGCCTGTGATCTCCAGGGGTCACTCAGGTTTGACTCAAAGGATCCAACAGCCTGTAGACCCTGTGCTTGAAGGCATGAGGGTCACCTCTGAGTTCACACTCACTAGTGTCCCTCCTTTCTTCAGAAAGCTAGGAACTGGGAAGACAAGGGGAAAATCAATCAAGGCCTGAGGTATGGGGCTGTAGGCTGGGAGGAAACTAACATTATTGAGAAGCTACTGATGTGAATACATTTCAATTACTACTCACATTGGTTTTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTTTTAAGACGGAGTTTTGCTCTCGTTGCCCAGGCTGGAGTGCAATGGAATGATCTAAGGTCACCACAACCTCCACCTCCCGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCGTGTGCCACCACACCCAGCTAAGTTTGTATTTTTTTAGTAGAGACGGTGTTTCACCATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCAAGTGATCCACCCACCTCGGCCTCCCAAAGTGCTGGGATTATAGGCATGAGCCACCACACCCAGCCTCACGTTGGTTTTTGAGATGGATTTTATTGCCATTTTGTACACAAAAAGGTCAAAACTCAGTGAGGTGAATTGACATGACAGTAAGTGAAAGAACTACTATCTGATTGGGGGTCTTCTGCCGCCTGCTCTGGGACTCTTTCTGCTATGACATGAAGGACATTGGCAACCCCAGTCCTTGCAGATTTCTTTCACTGTGTGC <class 'str'>