Difference between revisions of "Pharmacolyzer"
Farmakorakel (talk | contribs) (→Pharmacolyzer - Personalizing the PGx recommendations) |
Farmakorakel (talk | contribs) (→Examples of use) |
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|| NA19461 <br> NA19068 <br> NA20754 <br> NA21137 | || NA19461 <br> NA19068 <br> NA20754 <br> NA21137 | ||
|} | |} | ||
| − | running the | + | by running the commands on the form |
<pre>curl https://www.pgx.no/api/pharmacolyzer -d "patient_name=merged_patient&drugs=azathioprine&samples=NA19461"</pre> | <pre>curl https://www.pgx.no/api/pharmacolyzer -d "patient_name=merged_patient&drugs=azathioprine&samples=NA19461"</pre> | ||
| + | from the command line. | ||
For pretty printing, the following can be used: | For pretty printing, the following can be used: | ||
<pre>curl https://www.pgx.no/api/pharmacolyzer -d "patient_name=merged_patient&drugs=azathioprine&samples=NA19461" | python -m json.tool </pre> | <pre>curl https://www.pgx.no/api/pharmacolyzer -d "patient_name=merged_patient&drugs=azathioprine&samples=NA19461" | python -m json.tool </pre> | ||
Revision as of 09:26, 8 August 2018
Pharmacolyzer - Personalizing the PGx recommendations
In order to get personalized medication recommendations for a patient that has been sequenced, the Pharmacolyzer does multiple queries to the Pharmacoracle.
The starting point is a JSON file with a representation of the patient VCF in Manchester syntax provided by the Pharmacotyper.
We have coined the verb to pharmacolyze for the action of the Pharmacolyzer
Examples of use
We have downloaded a VCF with samples from the 1000 genomes project. Four samples from the VCF was then pharmacotyped and stored in a JSON file called merged_patient.json. Pharmacolysis can be performed for the following drugs and patient samples:
| Drugs | Samples |
|---|---|
| azathioprine clopidogrel |
NA19461 NA19068 NA20754 NA21137 |
by running the commands on the form
curl https://www.pgx.no/api/pharmacolyzer -d "patient_name=merged_patient&drugs=azathioprine&samples=NA19461"
from the command line. For pretty printing, the following can be used:
curl https://www.pgx.no/api/pharmacolyzer -d "patient_name=merged_patient&drugs=azathioprine&samples=NA19461" | python -m json.tool
