Alignment REST API
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0
Entering edit mode
16 months ago
joselu ▴ 110

Hello, I want to implement a rest api with python and requests to perform an alignment on Emboss needle https://www.ebi.ac.uk/Tools/psa/emboss_needle/

I have used the following code but I am getting the following error. I do not know what I'm doing wrong. Can somebody help me?

Thank you so much

import requests
base_url="https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/run"
auth_data = {'email': 'joseludenia@gmail.com'}
params={"asequence":"agtgctagggaggatcgggatgcgatgca" , "bsequence":"agtgcttggaggatcatgctaggatgca"}
response=requests.post(base_url, data=auth_data,  params=params)
id=response.text
res=requests.get(f"https://www.ebi.ac.uk/Tools/services/rest/emboss_needle/result/{id}/aln")
print(res.text)

ERROR

<?xml version='1.0' encoding='UTF-8'?>
<error>
 <description>Job 'emboss_needle-R20230322-062343-0348-8675423-p1m' is still running</description>
</error>
emboss rest-api alignment needle python • 861 views
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Entering edit mode
16 months ago
Shred ★ 1.5k

Why reinventing the wheel if they kindly give code for using their REST API? From https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBOSS+Needle+Help+and+Documentation#EMBOSSNeedleHelpandDocumentation-RESTAPI

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0
Entering edit mode

Yes, I agree, but is it possible to modify my code so that it doesn't return the error and keep waiting while the job is running? Thank you.

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0
Entering edit mode

Just check what they'd implemented so far in their script (for example, in the clientPool function).

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