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Wednesday, October 14, 2009

Useful error messages.... and another format rant.

I'll start with the error message, since it had me laughing, while everything else seems to have the opposite reaction.

I sent a query to Biomart the other day, as I often do. Most of the time, I get back my results quickly, and have no problems whatsoever. It's one of my "go-to" sites for useful genomic data. Unfortunately, every time I tried to download the results of my query, I'd get 2-3Mb into the file before the download would die. (It was a LONG list of snps, and the file size was supposed to be in the 10Mb ballpark.)

Anyhow, in frustration, I tried the "email results to you" option, whereupon I got the following email message:

Your results file FAILED.
Here is the reason why:
Error during query execution: Server shutdown in progress

That has to be the first time I've ever had a server shutdown cause a result failure. Ok, it's not that funny, but I am left wondering if that was the cause of the other 10 or so aborted downloads. Anyone know if Biomart runs on Microsoft products? (-;

The other thing on my mind this afternoon is that I am still looking to see my first Variant Call Format file for SNPs. A while back, I was optimistic about seeing the VCF files in the real world. Not that I can complain, but I thought adoption would be a little faster. A uniform SNP format would make my life much more enjoyable - I now have 7 different SNP format iterators to maintain, and would love to drop most of them.

What surprised me, upon further investigation, is that I'm also unable to find a utility that actually creates VCF files from .map, SAM/BAM, eland, bowtie or even pileup files. I know of only one SNP caller that creates VCF compatible files, and unfortunately, it's not freely available, which is somewhat un-helpful. (I don't know when or if it will be available, although I've heard rumours about it being put into our pipeline...)

That's kind of a sad state of affairs - although I really shouldn't complain. I have more than enough work on my plate, and I'm sure the same can be said for those who are actively maintaining SNP callers.

In the meantime, I'll just have to sit here and be patient... and maybe write an 8th snp format iterator.

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Blogger Josh said...

Back in the day, everyone wanted to use XML for all sorts of files/protocols (e.g., DAS). Personally, I'm glad that seems to have slowed, as XML isn't all that human-readable to me...

But the variety of file formats is still somewhat painful. I'm a bit tempted to try Google's "protocol buffers", or some other such standard binary encoding (I think there's a binary XML one, and ASN.1).

I've also just used Java serialization, but besides being Java-centric, I also still fairly often add a method, and can no longer read old objects, which is a pain.

October 15, 2009 8:51:00 AM PDT  
Blogger morin.ryan said...

SAMtools uses GLF to represent SNP calls. Who knows if this standard will become popular along with the SAM format, but it might be worth looking into. Here is a brief discussion of the format. There is a link to the spec somewhere in the SAM documentation as well.

October 16, 2009 11:20:00 AM PDT  
Blogger Anthony Fejes said...

Hi Ryan,

Given that Samtools has already included a link to the Variant Call format, (eg, in bold letters on the pileup page) I suspect that VCF will displace glf fairly rapidly even for Samtools. VCF also appears to be much more robust, although I'm sure there will always be someone with a dissenting opinion. (-:

And yes, politigenomics is an awesome blog - I should remember to read it more often.

October 16, 2009 11:27:00 AM PDT  

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