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Going to GOA, pt. 2: children of a lesser GO

The source file associated with this post can be downloaded here. The last time I talked about how to read a GOA gene_associations file into a Python dictionary data structure.  Our goal was to find all genes that are annotated as hydrolases in the GOA gene_associations file. The tricky part is, most enzymes are not […]

The Tao of Programming

I was recently reminded of this classic by Geoffrey James. Here are a few of my favorites. The whole text is available online. In the beginning was the Tao. The Tao gave birth to Space and Time. Therefore Space and Time are Yin and Yang of programming. Programmers that do not comprehend the Tao are […]

Thankful for…

In no particular order or context. No personal stuff and by no means a complete list: WordPress (like, duh). Wikipedia (default for looking up new stuff) Wikis in general (great lab management tool. Don’t need LIMS) Open Access Publishing and Creative Commons licensing. FLOSS licensing (90% of the software I use, and 100% of what […]

Short Bioinformatics Hacks: Glimmer Splitter

Glimmer is a program that predicts ORFs in bacterial and archeal genomes. The input is the assembled genome FASTA file, the output are several files of the predictions in different stages. The terminal output file is the .predict file. which looks something like this: >NODE_1_length_38001_cov_935.551880 orf00001 481      362  -2     1.45 orf00002      451      567  +1     0.59 […]

Short bioinformatics hacks, ch. 2: chunk it.

First, a non-bioinformatic one liner, which is very relevant to most of us working on 3 different machines simultaneously, not including the 80 in our cluster. ssh-ing and giving your password each time is painful, and makes it almost impossible to do scripted file transfers, like backups. A good solution is shared key ssh in […]

Short Bioinformatics Hacks, ch. 1

In any programming gig, and that includes bioinformatics, a lot of repeat scriptology comes cropping up. I decided to share some of that, pro publico bono, and also because I hope to start some sort of ongoing cookbook  for short bioinformatics hacks. If you have any cool short scripts you like to share, please email […]

Not dead, overloaded

When the Moon is in the Seventh House, and Jupiter aligns with Mars, a bunch of people gather for their “Bioinformaticians anonymous” group therapy. There they metaphorically gather, commiserating about how bioinformatics is dead (or was it bioinformaticians?), just smells funny or suffers from identity theft, probably because it got drunk at the last ISMB, […]