我的目标是从NCBI下载完整的后生动物基因组序列。我有我需要的基因组序列的唯一ID号列表。我计划使用Bio.Entrez模块EFetch下载数据，但今天通过2011年11月2日发行说明（http://1.usa.gov/1TA5osg）了解到EFetch不支持'Genome'数据库。谁能建议替代的软件包/模块或其他解决方法？先感谢您！
最佳答案
这是适合您的脚本-尽管您可能需要对其进行修补才能使其正常工作。可以根据自己的喜好为脚本命名，但是在调用脚本时，请按照以下步骤进行命名：
python name_of_script [扩展名为.py] your_email_address。
您需要将电子邮件添加到通话结束，否则将无法使用。如果您有登录号（1 /行）的文本文件，请选择选项2。如果选择选项1，它将要求您提供诸如生物体名称，菌株名称和关键字之类的项目。使用尽可能多的关键字-一定要用逗号分隔它们。如果使用第一个选项，将搜索NCBI并返回GI号[注意：NCBI正在9.2016中逐步淘汰GI号，因此此脚本可能在此之后不再起作用]，然后将其用于获取登录号。存在所有登录号后，将创建一个文件夹，并为每个登录号（称为登录号）创建一个子文件夹。在每个子文件夹中，将下载相应的fasta AND genbank文件。这些文件将带有登录号作为文件名（例如accession_number.fa，accession_number.gb）。根据您的目的编辑脚本。
还...请注意脚本的警告（ACHTUNG）部分。有时规则可能会弯腰...但是，如果您过于苛刻，则可能会阻止您的IP进入NCBI。你被警告了。
import os
import os.path
import sys
import re #regular expressions
from Bio import Entrez
import datetime
import time
import glob
arguments = sys.argv
Entrez.email = arguments[1] #email
accession_ids = []
print('Select method for obtaining the accession numbers?\n')
action = input('1 -- Input Search Terms\n2 -- Use text file\n')
if action == '1':
print('\nYou will be asked to enter an organism name, a strain name, and keywords.')
print('It is not necessary to provide a value to each item (you may just hit [ENTER]), but you must provide at least one item.\n')
organism = input('Enter the organism you wish to search for (e.g. Escherichia coli [ENTER])\n')
strain = input('Enter the strain you wish to search for. (e.g., HUSEC2011 [ENTER])\n')
keywords = input('Enter the keywords separated by a comma (e.g., complete genome, contigs, partial [ENTER])\n')
search_phrase = ''
if ',' in keywords:
keywords = keywords.split(',')
ncbi_terms = ['organism', 'strain', 'keyword']
ncbi_values = [organism, strain, keywords]
for index, n in enumerate(ncbi_values):
if index == 0 and n != '':
search_phrase = '(' + n + '[' + ncbi_terms[index] + '])'
else:
if n != '' and index != len(ncbi_values)-1:
search_phrase = search_phrase + ' AND (' + n + '[' + ncbi_terms[index] + '])'
if index == len(ncbi_values)-1 and n != '' and type(n) is not list:
search_phrase = search_phrase + ' AND (' + n + '[' + ncbi_terms[index] + '])'
if index == len(ncbi_values)-1 and n != '' and type(n) is list:
for name in n:
name = name.lstrip()
search_phrase = search_phrase + ' AND (' + name + '[' + ncbi_terms[index] + '])'
print('Here is the complete search line that will be used: \n\n', search_phrase)
handle = Entrez.esearch(db='nuccore', term=search_phrase, retmax=1000, rettype='acc', retmode='text')
result = Entrez.read(handle)
handle.close()
#print(result['Count'])
gi_numbers = result['IdList']
fetch_handle = Entrez.efetch(db='nucleotide', id=result['IdList'], rettype='acc', retmode='text')
accession_ids = [id.strip() for id in fetch_handle]
fetch_handle.close()
if action == '2': #use this option if you have a file of accession #s
file_name = input('Enter the name of the file\n')
with open(file_name, 'r') as input_file:
lines = input_file.readlines()
for line in lines:
line = line.replace('\n', '')
accession_ids.append(line)
#--------------------------------------------------------------------------------------------------------------
#----------------------------------- Make directory to store files --------------------------------------------
new_path = 'Genbank_Files/'
if not os.path.exists(new_path):
os.makedirs(new_path)
print('You have ' + str(len(accession_ids)) + ' file(s) to download.') #print(accession_ids)
ending='.gb'
files = []
##CHECK IF FILE HAS BEEN DOWNLOADED
for dirpath, dirnames, filenames in os.walk(new_path):
for filename in [f for f in filenames if f.endswith(ending)]: #for zipped files
files.append(os.path.join(dirpath,filename))
for f in files:
f = f.rsplit('/')[-1]
f = f.replace('.gb', '')
if f in accession_ids:
ind = accession_ids.index(f)
accession_ids.pop(ind)
print('')
print('You have ' + str(len(accession_ids)) + ' file(s) to download.')
#--------------------------------------------------------------------------
###############################################################################
#---ACHTUNG--ACHTUNG--ACHTUNG--ACHTUNG--ACHTUNG--ACHTUNG--ACHTUNG--ACHTUNG----#
###############################################################################
# Call Entrez to download files
# If downloading more than 100 files...
# Run this script only between 9pm-5am Monday - Friday EST
# Send E-utilities requests to http://eutils.ncbi.nlm.nih.gov
# Make no more than 3 requests every 1 second (Biopython takes care of this).
# Use URL parameter email & tool for distributed software
# NCBI's Disclaimer and Copyright notice must be evident to users of your service.
#
# Use this script at your own risk.
# Neither the script author nor author's employers are responsible for consequences arising from improper usage
###############################################################################
# CALL ENTREZ: Call Entrez to download genbank AND fasta (nucleotide) files using accession numbers.
###############################################################################
start_day = datetime.date.today().weekday() # 0 is Monday, 6 is Sunday
start_time = datetime.datetime.now().time()
print(str(start_day), str(start_time))
print('')
if ((start_day < 5 and start_time > datetime.time(hour=21)) or (start_day < 5 and start_time < datetime.time(hour=5)) or start_day > 5 or len(accession_ids) <= 100 ):
print('Calling Entrez...')
for a in accession_ids:
if ((datetime.date.today().weekday() < 5 and datetime.datetime.now().time() > datetime.time(hour=21)) or
(datetime.date.today().weekday() < 5 and datetime.datetime.now().time() < datetime.time(hour=5)) or
(datetime.date.today().weekday() == start_day + 1 and datetime.datetime.now().time() < datetime.time(hour=5)) or
(datetime.date.today().weekday() > 5) or len(accession_ids) <= 100 ):
print('Downloading ' + a)
new_path = 'Genbank_Files/' + a + '/'
if not os.path.exists(new_path):
os.makedirs(new_path)
handle=Entrez.efetch(db='nucleotide', id=a, rettype='gb', retmode='text', seq_start=0)
FILENAME = new_path + a + '.gb'
local_file=open(FILENAME,'w')
local_file.write(handle.read())
handle.close()
local_file.close()
handle=Entrez.efetch(db='nucleotide', id=a, rettype='fasta', retmode='text')
FILENAME = new_path + a + '.fna'
local_file=open(FILENAME,'w')
local_file.write(handle.read())
handle.close()
local_file.close()
else:
print('You have too many files to download at the time. Try again later.')
#-------
关于python - 可替代Bio.Entrez EFetch从NCBI下载完整基因组序列，我们在Stack Overflow上找到一个类似的问题：https://stackoverflow.com/questions/37448144/