It seems like the forces of light have triumphed somewhere around September 2006: …as have their evil counterparts, April 2009: bacteria are neck-in-neck with humans: But they beat the largest creatures on Earth: Of course, you can’t beat cats:
There has been a lot of discussion recently on this blog and others on the need for robust scientific software. Most of the discussion I have been involved in comes from bioinformaticians, because, well, I am one. There has been plenty of talk about code robustness, sharing, and replicability vs. reproduciblity. I do not want [...]
I just learned about this one: ROSALIND is a really cool concept in learning bioinformatics. You are given problems of increasing difficulty to solve. Start with nucleotide counting (trivial) and end with genome assembly (not so trivial). To solve a problem, you download a sample data set, write your code and debug it. Once [...]
Genomics is a new and exciting programming language based on Brainfsck. Here are the commands: g Move pointer to the right. e Move pointer to the left. n Increment the cell at the pointer. o Decrement the cell at the pointer. m Jump forward past the matching i if the cell at the current pointer [...]
If you have a merged file of paired-end reads, here is a quick way to read them using Biopython: from Bio import SeqIO from itertools import izip_longest # Loop over pairs of reads readiter = SeqIO.parse(open(inpath), “fastq”) for rec1, rec2 in izip_longest(readiter, readiter): print rec1.id # do something with rec1 print rec2.id # do something [...]
Warning: NSFW language. Brainfuck is a Turing-complete programming language consisting of eight commands, each of which is represented as a single character. > Increment the pointer. < Decrement the pointer. + Increment the cell at the pointer. – Decrement the cell at the pointer. . Output the ASCII value of the cell at the pointer. [...]
So you received your mate-paired reads in two different files, and you need to merge them for your assembler. Here is a quick Python script to do that. You will need Biopython installed. #!/usr/bin/env python from Bio import SeqIO import itertools import sys import os # Copyright(C) 2011 Iddo Friedberg # Released under Biopython [...]
…you find this on the top of the paper pile on his desk:
I’m organizing a workshop later this month (see here, scroll to session V), and I have just received the attendees list from the main conference’s organizers. Since I need to spam send the attendees informative email on the specific workshop, I needed their email addresses. Here’s what I did. The file itself is MS Word [...]
In celebration of the biohackathon happening now in Tokyo, I am putting up a script that is oddly missing from many bioinformatic packages: extracting intergenic regions. This one was written together with my student, Ian. As for the biohackathon itself, I’m not there, but I am following the tweets and Brad Chapman’s excellent posts: Day [...]
A nice take on the vi / emacs wars Also, real programmers browse the web using the vimperator.
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 [...]
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 [...]
