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Update: UniCurses on Windows

jcole — Fri, 30 Sep 2011 02:22:01 +0000

A quick update to my earlier post about getting UniCurses working on Windows — for some reason, it works as described with Python 3.1, but not 2.5 (I know, I’m a little behind). I’ll get it sorted out one of these days.

Edit: You know, reading is a wonderful thing. It says right here that UniCurses requires v2.6.1 or higher. Good grief.

Library Solutions for Homeschoolers

jcole — Sat, 13 Aug 2011 18:26:46 +0000

Recently, Misty and I were talking about solutions to one of the perpetual problems faced by homeschoolers: keeping the library organized. (Hint: if you homeschool and do not have a library, you’re doing it wrong.) Anyway, I dug out my old PS/2 :CueCat and used it to add a few books to Tellico and Data Crow, which are Open Source desktop applications for managing collections. That worked nicely, but I ran into two challenges: 1) I would prefer that the data be accessible from pretty much anywhere, and 2) my laptop doesn’t have a PS/2 port, so I need a USB :CueCat (they do exist).

With respect to point 1, I have a web application that I’ve been writing and rewriting for years now that works okay, but doesn’t have any of the fancy JavaScripty/AJAXy bits that let it properly parse :CueCat input, so I’d have to add another feature when there already are so many that don’t work as intended, and I have so much free time.

While Google-ing around to address point 2, I found what is basically a turn-key solution for $40. Not super-cheap, but not bad that all. For that you can get an unlimited lifetime LibraryThing account — good grief, someone on there has over 45,000 books in their library — and a USB :CueCat for convenient data entry. I remembered that I had an account there already, which lets you enter up to 200 books, and confirmed that my PS/2 :CueCat works like a charm with the site. Thing One objected to the idea that he spend the next week carrying the books down from upstairs, scanning them, and putting them away, so a USB scanner that can be connected to Misty’s or my laptop seems to be a worthwhile investment.

I’m not saying that my time is worth millions, or that there is anything wrong with learning new skills, but for a pretty meager amount of money I can get everything organized pretty quickly with a minimal amount of work. LibraryThing is about 20 times cooler than my tool, even if I didn’t write it and it’s quite fast. You can’t beat that with a stick, I tell you what.

So, I think that we have a solution to our problem.

Lyx 2 and Sweave on Windows

jcole — Sun, 12 Jun 2011 17:42:22 +0000

Just a quick not to say that I just got Lyx and Sweave working under Windows XP. Maybe I’ll post some links later, but for now I just wanted to say that it was pretty straightforward. I installed R 2.12, the current version of Rtools, and Lyx 2, as well as updating my MiKTeX installation. The only problem that I had was that I that I copied Sweave.sty into the wrong place in my C:\texmf tree. Once I got that sorted, it works like a charm.

Maybe I should add Sweave output to PyPedal…

I guess that nobody has been using that feature (2.0.1 bugfix release)

jcole — Thu, 30 Dec 2010 14:44:59 +0000

Today I released PyPedal version 2.0.1, which includes a bugfix to the inbreeding routine. PyPedal will form a numerator relationship matrix (NRM) at the time the pedigree is loaded if you ask it to. and the NRM can then be used to find things such as coefficients of inbreeding. The inbreeding routine checks the pedigree to see if there is already an attached NRM, and if there is uses it rather than performing de novo calculations. There was an indexing bug in that part of the code that resulted in coefficients of inbreeding being assigned to the wrong animal. That has been fixed, and a stray debugging message also has been properly wrapped so that it won’t pop-up when it’s not supposed to.

Happy New Year!

Everyone said I was daft to build a castle on a swamp, but I built it all the same, just to show them.

jcole — Wed, 29 Sep 2010 19:07:55 +0000

The day they said would never come has finally arrived — just a few minutes ago I tagged and released the first production version of PyPedal, my pedigree analysis software. This is the end of a seven-and-a-half-year development cycle, which included a Google-esque five-year beta period. The first dated entry in my 2,117-line CHANGES.txt file is from April 6, 2003, which is when I began the rewrite of PyPedal 1 (never released). There is a big gap in my log, with the next entry from March 31, 2004, relating to the handling of sires and dams with no pedigree file entry. Development was fitful, and you can see what particular things I was interested in at a given time by the clustering of topics in the changefile, which is probably pretty typical of open source projects with a very small user-base.

While I don’t know of many people using PyPedal I have benefited from the feedback of several users over the past several years, particularly Matthew Kelly, Dan Cieslak, and Matthieu Authier. A number of interesting features have been added because of their input, and some nasty bugs fixed, as well. I hope that people will continue to contribute bug report and feature requests.

So what’s next for PyPedal? Well, there will certainly be 2.0.x maintenance releases for bugfix purposes. There also will be a 2.1 development branch, which will focus on (in no particular order):

Some novel tools for manipulating pedigrees — extracting individuals or groups of animals, merging pedigrees, that kid of thing.
Better visualization tools, particularly for large pedigrees.
Improved documentation, particularly in the code itself.
Performance improvements, particularly in the inbreeding routines.

I guess that’s all I have to say for now. If you’re one of my users, thanks very much! If you’re not one of my users, there’s no time like the present to start using PyPedal.

Unknown Parent Groups and PyPedal

jcole — Fri, 17 Sep 2010 17:36:26 +0000

I had a visiting scientist in the lab the last couple of weeks and had to get a manuscript finished. But here we are again. Here’s the deal — no unknown parent groups in version 2.0. It turns out to be harder to do well that I first thought, so rather than do a poor job I decided to punt it. However, I’m not going to leave you hanging, so the 2.0 release will come with only two three small fixes:

Change the processing of ASD pedigrees to use hashlib instead of the md5 module. This may result in user-selectable hash functions in the event that you have trouble with collisions.
For some reason, the logfile is not being created properly. That needs fixed.
The NewPedigree::save() method is going to get a new argument so that you can specify the format of the output file.

So, okay, less talking and more coding.

So, what’s the deal with PyPedal?

jcole — Sun, 05 Sep 2010 18:20:00 +0000

I’m glad you asked that. If you’ve seen the website recently then you know that there’s been no development activity for quite a long time. What can I say? I’ve been pretty busy on other things. The important point is that PyPedal is not abandonware.

On September 1, 2010, I uploaded Release Candidate 9 and let it go into the wild. In addition to adding GENES 1.20 input and output, the changes include some minor documentation updates and a few small code fixes.

In Release Candidate 10, which will be released this week, all I’ve done is add an option to pyp_nrm.fast_a_matrix() to add coefficients of inbreeding read from the pedigree file to the diagonal elements for founders when forming the relationship matrix. I need to update the documentation and check the files once more because I think that there are still some stray hard-coded debugging messages which need to be removed.

The only other thing I’m thinking of adding is support for unknown parent groups, and possibly adding methods to the NewPedigree class that support adding (merging) and subtracting (splitting) pedigrees, but I think that’s going to get punted to the 2.1 development branch because it’s a much harder problem than it may sound on the surface.

I still need bug reports and feature requests. I’ll do my best to fix bugs promptly. I can’t make any promises about feature requests. My thinking right now is that I need to focus on polishing things. The demographics (pyp_demog), graphics (pyp_graphics) and reporting (pyp_reports) modules all could use a lot of fine-tuning to make them more useful. The documentation always needs work. I’m still concerned about the implementation of the algorithms in pyp_metrics for calculating effective ancestor numbers. They’re much less fun that implementing new features, but probably necessary. And then there’s the whole issue of dense SNP data…

ElleryPedia

jcole — Sat, 19 Jun 2010 18:29:45 +0000

Can’t get enough of Thing One’s wit and wisdom? Visit ElleryPedia for more!

Moved to new host

jcole — Wed, 20 May 2009 02:58:54 +0000

I’ve moved from Godaddy to MochaHost. Everything seems to be working okay, and now I can get some Django going.

PyPedal Article Published in Python Magazine

jcole — Mon, 30 Mar 2009 13:04:28 +0000

The March 2009 issue of Python Magazine is on the news-stands. Guess whose article is mentioned on the cover?

Python Magazine, March 2009