Feature request: Querying SNP addresses

[mgenphl]

Hello.

I have not found any way of querying the SNP addresses within the code. I have to manually query the Postgres database. I would be happy to work on a PR if you like.

Thank you.

Anders.

[Wang-Jing-NZ]

we have been writing our own python scripts for querying the db. It depends on how you want to use the information in the db with other data sources.

[timdallman]

Hi.
We've actually just added a sub-routine called get_strains - tag v1.0.4.
This will return all isolates in the database with their SNP Address (or just the isolates from a requested SNP cluster).
See if that meets your requirements if not always happy to receive a pull request.
Similar to Jing we also have a raft of scripts that query the postgres database to integrate the data into our surveillance systems.
Best wishes
Tim

[andersgs]

Thank you both for your replies.

I'll install the latest version, and see how it goes.

In my mind, I was expecting something along the lines:

snapperdb query --isolate ID --address 250:100:50:25:*: *: * meaning give me all isolates within 10 SNPs from isolate ID.

snapperdb query --address 250:100:50:25:*:*:* might mean "give me all clusters with 10 SNPs".

I would have to speak to some our Epis to understand what other queries they may have, but at least the functionality of some basic querying of this nature would be a great feature to add.

There might be also an option to output the aligment of the clusters...

Best. Anders.