Downloads

pATLAS database requests can be done through URLs, similar to what is done in eutils .
Download metadata
From a browser
If you have a list of accession numbers present in pATLAS database, you can download all metadata through:
http://www.patlas.site/api/sendmetadata/?accession=<accession_list>
or
http://www.patlas.site/api/sendmetadata?accession=<accession_list>
It will fetch an array of json objects in which each contains all metadata available for that accession number.
E.g.:
http://www.patlas.site/api/sendmetadata?accession=NC_017393_1,NZ_CP009835_1
From a terminal
TL;DR
import requests
​
r = requests.post("http://www.patlas.site/api/sendmetadata/",
json=["NC_017393_1", "NZ_CP009835_1"])
​
r.content
# your results
Explanation
Send the post to http://www.patlas.site/results/.
Send a json with the request. This json must contain a list of
accession numbers
Download sequences
The sequences of plasmids from pATLAS database can be downloaded through the following API when providing a list of the accession numbers:
http://www.patlas.site/api/senddownload/?accession=<accession_list>
It will generate a fasta file with the accession numbers requested and the sequences associated with each accession number.
Limitation: This type of request to pATLAS database cannot have thousands of accessions therefore for requests with thousands of accessions, use the following request type:
Python:
import requests
​
# Note that form data should be sent as a string and using 'data' instead of 'json'
r = requests.post("http://www.patlas.site/api/senddownload/",
data={"accessions": '["NC_017393_1", "NZ_CP009835_1"]'})
​
r.content
# result: http://patlas.site/results?query=15675682358507007771
Javascript / JQuery:
// Note that form data should be sent as a string
$.post("www.patlas.site/api/senddownload/", {"accessions": JSON.stringify(["NC_017393_1", "NZ_CP009835_1"])}, (data, status) => {
      if (status === "success") {
        console.log(data)
        // result: http://patlas.site/results?query=15675682358507007771
      }
    }
  )
Note - The download button in the top bar downloads the accession numbers associated with the current selection using this last API, so it is possible to download the full pATLAS data set. See Top navigation bar for more information. Download button in table also uses this API.

Antibiotic and plasmid family detection

Import files

Last modified 4yr ago