SNP Datatabase v0.1
Good news, my snp database seems to be in good form, and is ready for importing SNPs. For people who are interested, you can download the Vancouver Short Read Package from SVN, and find the relevant information in
/trunk/src/transcript_analysis/SNP_Database/
There's a schema for setting up the tables and indexes, as well as applications for running imports from maq SNP calls and running a SNP caller on any form of alignment supported by FindPeaks (maq, eland, etc...).
At this point, there are no documents on how to use the software, since that's the plan for this afternoon, and I'm assuming everyone who uses this already has access to a postgresql database (aka, a simple ubuntu + psql setup.)
But, I'm ready to start getting feature requests, requests for new SNP formats and schema changes.
Anyone who's interested in joining onto this project, I'm only a few hours away from having some neat toys to play with!
/trunk/src/transcript_analysis/SNP_Database/
There's a schema for setting up the tables and indexes, as well as applications for running imports from maq SNP calls and running a SNP caller on any form of alignment supported by FindPeaks (maq, eland, etc...).
At this point, there are no documents on how to use the software, since that's the plan for this afternoon, and I'm assuming everyone who uses this already has access to a postgresql database (aka, a simple ubuntu + psql setup.)
But, I'm ready to start getting feature requests, requests for new SNP formats and schema changes.
Anyone who's interested in joining onto this project, I'm only a few hours away from having some neat toys to play with!
Labels: Algorithms, Aligners, Bioinformatics, Code planning, documentation, formats, Genomics, SNP calling, SNP Database, SNPS, Software
5 Comments:
Wheeh, toys. Looking forward to it!
-- Oliver
This probably isn't very helpful but I have done something similar for importing MAQ and Newbler output for bacterial genome mapping runs. In this case importing into a Postgres database and displaying via a web interface built in Python. Can you think of any way of helping unify efforts without slowing either of us down? I'll stick the code into git so you can have a look.
Hi Nickloman,
Off hand, two things seem to be very helpful that you could do.
The first is to see if your web interface would work on the same database. I won't be able to work on anything on the web end for a while, so any progress you can make on that would be a massive help.
The other thing that would be useful would be to work on SQL statements for retrieving results.
If either of those sound like a good way to get involved, I'm more than happy to add you to the project.
Feel free to find me on MSN or Google Talk.
Anthony
OK! I'll try and MSN you about it but for some reason adding your email address doesn't seem to find you ...
Sorry - my MSN account is under the address: apfejes@uwaterloo.ca. It's no longer a valid email account, so don't try to email me there.
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