Ettema lab blog

Finding overlapping ranges in Perl

Finding if a value is in a range is something you come across quite often. For instance, perhaps you want to see if a sequence is in a particular region. Or in my case it is to find if two genes overlap. One could solve this in a lot of different ways, but the one

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Jennah joins the Ettema-lab

I am happy to announce that Jennah Dharamshi has joined the ettema-lab as a PhD student per Januari 1st! Jennah will work on the  exploration of novel microbes that reside in the environment, so-called ‘microbial dark matter’. To do so, she will use novel cultivations-independent techniques such as metagenomics and single-cell genomics, but also more

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Defensive BASH

Ran across this interesting blog post talking about defensive BASH scripting. There might be some things one might not agree with, but it do contain a lot of tips for good practices. The idea behind the name “defensive” is to write code that will run into as few of a problems as possible. I for

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Summary of Spang et al.

Farshid Jalalvand, who runs the blog ‘Ytterst Upphöjda Observationer’, made a very nice summary of the recent EttemaLab Spang et al. paper. He has provided a good background to phylogenetics and it very well worth the read for all you Swedish speaking people out there. You can find his blogpost here

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Using for loop vs Gnu parallel for BLAST

I recently ran across a issue when I had to run a lot of small blasts (1000+) of a bunch of files against a common database, and was thinking about how to do this efficiently. My first approach was to loop over all the files I wanted to blast and run them with the -num_threads

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Extracting information from GenBank files

Sometimes you want to get a quick overview of the distribution of a group of uncultured microorganisms. In my case I had extracted all the 16S sequences classified as a certain clade, from the Silva database, and I wanted to know which environment they came from. This information can easily be found in the GenBank

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Mounting drives on OSX over ssh

My computer setup at work consists of a workstation running Linux, and a macbook. In a way to make things smoothly I wanted a way to automatically mount a drive from my Linux machine on my macbook so I can easily share files between the computers. A really nice way of doing this is using

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Inverse removing files from a directory

One thing I really like about bash is how certain problems can be solved in a multitude of ways. Recently I had the following problem. A directory contain a whole bunch of files like this:

In reality there were thousands of files, and also some non html files, but let’s just keep it simple

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Reference notes on Bash, Perl, BioPerl, R, Python, Git, Beskow, Uppmax and various Bioinformatics Tools

Hej all, During the last 2,5 years I’ve been trying to write down what I have learned every time I learned something new “code” related. I have just published these notes on github for the world to see. Though they are probably written in such a way that I would understand them but not necessarily

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Disa joins the lab

Disa Bäckström has joined the Ettema lab! Disa, who did her master thesis at the lab earlier this year, has joined the lab as a PhD student! Disa will work on the genomic exploration of ‘microbial dark matter’, focusing on new archaeal lineages and viruses, using both lab- and bioionformatics-based approaches. Welcome Disa! /TE  

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