Comments on: SNPFile

By: gua sha

gua sha — Wed, 11 Mar 2009 09:46:55 +0000

I really liked the way they came off

By: Thomas Mailund

Thomas Mailund — Thu, 08 Jan 2009 16:55:03 +0000

We wrote the converters before we made the Python interface. These days, I would write such things as scripts instead.

Sorry to confess, we haven’t written a manual for the Python interface yet :-(

By: gioby

gioby — Thu, 08 Jan 2009 16:47:15 +0000

thanks!
It works: I can confirm that the deb package installs correctly on an Ubuntu Hardy 8.04.
It seems nice to have the parsers to convert it from other existing formats like fastPhase etc.

By: gioby

gioby — Thu, 08 Jan 2009 16:46:26 +0000

thanks!
It works: I can confirm that the deb package installs correctly on an Ubuntu Hardy 8.04.

By: Thomas Mailund

Thomas Mailund — Thu, 08 Jan 2009 16:18:35 +0000

No, wait, I see the problem with the URL: the ∼ is not the same character as ~. If you’ve cut the link from the PDF, it uses the wrong tilde.

By: Thomas Mailund

Thomas Mailund — Thu, 08 Jan 2009 16:08:23 +0000

The link is correct, but I think there is something wrong with the server. I cannot access other parts of my home page right now :(

By: gioby

gioby — Thu, 08 Jan 2009 15:48:16 +0000

You are welcome :)

p.s. it seems that BMC Bioinformatics hasn’t published the full article yet. It says that ‘the fully formatted PDF and HTML versions are in production’, so I can’t access to any supplementary data.
Moreover, the link posted in the article (http://www.daimi.au.dk/∼mailund/SNPFile/) doesn’t seem to work (it says ‘Page not found’).
So nothing, there is no way to see the code.

By: Thomas Mailund

Thomas Mailund — Thu, 08 Jan 2009 14:45:51 +0000

Thanks, I’ll have a look at the discussion :)

By: gioby

gioby — Thu, 08 Jan 2009 14:38:57 +0000

I was proposing to adopt your binary format to the biopython mailing list.
The population genetics module in biopython is in its earlier phases of development, so I thought it could be a good idea to propose its adoption or at least to include an handler for your format.

Why don’t you have a look at the discussion on the mailing list?
- http://lists.open-bio.org/pipermail/biopython/2008-December/004830.html

By: Thomas Mailund

Thomas Mailund — Wed, 07 Jan 2009 09:00:34 +0000

Hi gioby,

A main difference between SNPFile and those formats you mention is that SNPFile is explicitly designed to store genetic data whereas the others are more general frameworks. So we can optimize our data storage to the access patterns typical for our use. To which degree you can do that with the other frameworks, I don’t really know.

As for the testing, the unit tests are provided with the code. Of course there are no guarantees that there are no bugs (I am willing to guarantee that there is) and no guarantees that you will not lose data. This is academic software provided for free, so that is the deal, as always.

We have used it for the last two years with very few problems, that is all I can say :)