30Apr/090
Thanks for a great term
Just wanted to thank my students, all ~44 of you, for putting up with my stammering explanations of genetics. I sure learned a ton and I hope you did too. Good luck with your finals.
30Apr/090
RegEx to id comma-space(s) or space(s) delimited text
I'm not all that great at RegEx, but I needed split a line of text on commas followed by spaces and/or by spaces (including tabs). 30 minutes later after swearing and sweating with iPython, I produced the following little expression. Who needs the CSV module?
re.compile(',(?:\s*)|\s*')
Example Usage:
OOE: Another blog I help write
- From Tophat to Pysam July 21, 2010I recently needed to interact with a SAM file in python that was created as part of a Tophat run. Rather rolling my own parser I decided to use the handy pysam module. However, I immediately ran into trouble. I couldn’t get pysam to open my file. It turns out pysam requires a BAM file not a SAM file. This meant I need to convert filetypes. So, I fired up sa […]
- Inferring Heterozygosity from SNP data April 20, 2010This looks straightforward. n = total number of reads aligning to a base y = total number of reads aligning to a base that match the reference p = probability that reads match the reference base Bases with LOD>3 were called SNPs or sites of heterozygosity. From Bloom et al. (2009) Measuring differential gene expression by short read sequencing: quantitat […]
- Why we are "Python Fanboys" April 15, 2010I think I can safely say that we’re all Python evangelists. In fact, I’m pretty sure my first conversation with ‘FixedByDrift’ revolved around just how enamored with Python he is. Likewise my first email with ‘AmbiguousBase’ was a code exchange of microsatellite finding software written in Python. We just love Python. So why should you learn to love Python […]
Web Favs via GReader
- Does England Just Need a Good Shag?Published: June 22, 2010Things are not looking good for England. Two draws against opponents many in the global football community had quickly written off. The passes aren’t coming through, the runs are being cut off, the set pieces...
- Environmental change enhances cognitive abilities in fish.Published: April 26, 2010Source: pubmed: "plos biology"[jour]My Note: Clearly it's important to eat well.Environmental change enhances cognitive abilities in fish. PLoS Biol. 2010;8(4):e1000351 Authors: Kotrschal A, Taborsky B Flexible or innovative behavior is advantageous, espe...
- Version Control FailurePublished: April 8, 2010Source: Omics! Omics!My Note: This is moderately terrifying. Luckily, there is only one anole genome version publicly available at this point in time.Well, it was inevitable. A huge (and expensive) case of confused human genome versions.While the human genome is 10 years old, that was hardly the final word. Lots of mopping up remained on the original proj...
- See all shared items
- Plugin by C. Murray Consulting
Evolution
People
Recent Posts
- MultiMarkdown
- Vertebrate Zoology: Bi302
- 40 Essential Tools and Resources to Visualize Data | FlowingData
- Wallace’s Insect Collection Found!
- Blue Collar Bioinformatics
