Submitting through the web service

Multiple sequences can be submitted in bulk using a simple POST mechanism. The results are a tab-delimited table.

Input

Sequence and snvlist files

The following fields are required for sequence or snvlist queries. These must be stored in a file for upload using the multipart/form-data protocol:

• file - a file upload
• fileType - set this to "sequences" or "snvlist" depending on the format. See SNV Query tab for accepted formats.

Genbank identifiers

Genbank queries can use a simple GET mechanism using the gb argument:
https://mitomap.org/mitomaster/websrvc.cgi?gb=JX153710.1&output=summary

Output

Output is specified by the output argument

• output => 'detail' - very similar to the detail page shown in the Mitomaster web application, with a line for each mutation (default)
• output => 'summary' - very similar to the summary page shown in the Mitomaster web application, with a line for each sequence
• output => 'hsd' - variants in a HaploGrep-compatible .hsd file format

Perl client example

#!/usr/bin/perl
use LWP::UserAgent;
use HTTP::Request::Common;

my $userAgent = LWP::UserAgent->new(timeout => 1800); #a half-hour

#fileType can be sequences or snvlist
my $request = POST 'https://mitomap.org/mitomaster/websrvc.cgi',
    Content_Type => 'multipart/form-data',
    Content => [ file => ['mySequences.fasta'], fileType => 'sequences', output => 'detail'];

my $response = $userAgent->request($request);
print $response->error_as_HTML . "
" if $response->is_error;

if ($response->is_success) {
     print $response->decoded_content;
} else {
     die $response->status_line;
}

Python2 client example

#!/usr/bin/env python2
from poster.encode import multipart_encode
from poster.streaminghttp import register_openers
import urllib2

register_openers()

#fileType can be sequences or snvlist
datagen, headers = multipart_encode({"file": open("mySequences.fasta"),'fileType':'sequences','output':'detail'})

request = urllib2.Request("https://mitomap.org/mitomaster/websrvc.cgi", datagen, headers)
try:
     print urllib2.urlopen(request).read()
except urllib2.HTTPError, e:
     print "HTTP error: %d" % e.code
except urllib2.URLError, e:
     print "Network error: %s" % e.reason.args[1]

Python3 client example

#!/usr/bin/env python3
import requests

try:
    response = requests.post("https://mitomap.org/mitomaster/websrvc.cgi", files={"file": open("mySequences.fasta"),'fileType': ('', 'sequences'),'output': ('', 'detail')})
    print(str(response.content, 'utf-8'))
except requests.exceptions.HTTPError as err:
    print("HTTP error: " + err)
except:
    print("Error")