[BioRuby] May I contribute a 23andMe flatfile parser?

Naohisa GOTO ngoto at gen-info.osaka-u.ac.jp
Fri Oct 1 10:01:51 UTC 2010

Hi Russell,

Please do so. No one has right to prohibit development.
No response from anyone for a week suggest that it does not exist.

In BioRuby, no data class for a SNP. Writing general SNP class,
not specific to 23andMe, may also be needed during the development
of the parser.

I found the data format description and sample data in SNPedia.
It seems it is a simple tab-separated text. Is it the
"23andMe SNP/genotype flatfile" you wrote?


Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org

On Fri, 24 Sep 2010 03:34:06 -0400
Russell Whitaker <russell.whitaker at gmail.com> wrote:

> Hi all / はじめまして、みんなさん。。。
> [Please let me know if my Japanese is mojibake / 文字化け]
> I'm a former professional software engineer who left Google 3 years
> ago to pursue a degree in biochemistry from Columbia University (which
> I did in fact complete, 4 months ago). After having programmed other languages
> over a nearly 20 year career - one in Japan, by the way - I switched from
> Python to Ruby/Rails at Google, and have committed to continue with that
> as primary platform (except for statistical applications, for which I'm doing R
> when needed).
> I've been researching best platforms for going general bioinformatics
> work, and of course discovered BioRuby, which is why I'm here on this list.
> A few hours of digging have convinced me that a 23andMe SNP/genotype
> flatfile parser does not yet exist in BioRuby. However, I may be wrong, so I'll
> ask: does one exist? No mention of "23andMe" exists in the list archives.
> Would anyone object to my writing one? I've been familiarizing myself with
> the development process for this group, e.g.:
> http://lists.open-bio.org/pipermail/bioruby/2010-June/001319.html
> I already have a GitHub account, of course.
> Thanks in advance for your help, and I look forward to contributing to this
> project.
> よろしくおねがいたします、
> ラッセル
> -- 
> Russell Whitaker
> http://twitter.com/OrthoNormalRuss
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