我试图从UniProt获得一些结果,这是一个蛋白质数据库(细节并不重要).我正在尝试使用一种从一种ID转换为另一种ID的脚本.我能够在浏览器上手动执行此操作,但无法在Python中执行此操作.
在http://www.uniprot.org/faq/28中有一些示例脚本.我尝试了Perl,它似乎工作,所以问题是我的Python尝试. (工作)脚本是：
## tool_example.pl ##
use strict;
use warnings;
use LWP::UserAgent;
my $base = 'http://www.uniprot.org';
my $tool = 'mapping';
my $params = {
from => 'ACC',to => 'P_REFSEQ_AC',format => 'tab',query => 'P13368 P20806 Q9UM73 P97793 Q17192'
};
my $agent = LWP::UserAgent->new;
push @{$agent->requests_redirectable},'POST';
print STDERR "Submitting...\n";
my $response = $agent->post("$base/$tool/",$params);
while (my $wait = $response->header('Retry-After')) {
print STDERR "Waiting ($wait)...\n";
sleep $wait;
print STDERR "Checking...\n";
$response = $agent->get($response->base);
}
$response->is_success ?
print $response->content :
die 'Failed,got ' . $response->status_line .
' for ' . $response->request->uri . "\n";
我的问题是：
1)你会如何在Python中做到这一点？
2)我能够大规模“缩放”那个(即在查询字段中使用大量条目)吗？
最佳答案
问题#1：
这可以使用python的urllibs完成：
import urllib,urllib2
import time
import sys
query = ' '.join(sys.argv)
# encode params as a list of 2-tuples
params = ( ('from','ACC'),('to','P_REFSEQ_AC'),('format','tab'),('query',query))
# url encode them
data = urllib.urlencode(params)
url = 'http://www.uniprot.org/mapping/'
# fetch the data
try:
foo = urllib2.urlopen(url,data)
except urllib2.HttpError,e:
if e.code == 503:
# blah blah get the value of the header...
wait_time = int(e.hdrs.get('Retry-after',0))
print 'Sleeping %i seconds...' % (wait_time,)
time.sleep(wait_time)
foo = urllib2.urlopen(url,data)
# foo is a file-like object,do with it what you will.
foo.read()