Cleaning up with sed 2

I have a list of nucleotide sequences in fasta format, obtained from NCBI. I want to clean the sequences names, leaving only the accession numbers. Additionally, I want to extract the accession numbers to a separate list. I am not that familiar with sed, since I use it mainly in my SlackBuilds to fix small things. Therefore, for my fuuture reference, I decided to sum things up.
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FASTA syntax highlight

FASTA is among the most common text formats for nucleotide or amino acid sequences. I use medit and a feature that I have been looking for is a syntax highlighting for FASTA files. I want to have colour code for nucleotides and amino acids, similarly to how scripting or programming languages are displayed by the editor. I have been looking for this feature for a long time and all I found was the fasta.lang at GNOME’s wiki and the fastalang at git. Both projects are for Gedit and support only nucleotide sequences. Let’s say neither of these did the job for me, but I appreciate very much both projects. I decided to do things myself.
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xflock4: lock the screen

I am using XFCE and I want to have an entry in the menu that will lock the screen. The command that locks the screen in XFCE is

xflock4

yes… it took me some time to figure it out. Anyway, from here it is quite straightforward. I made the following xflock4.desktop file:
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Five years for Slackalaxy

It has been 5 years! I have 156 posts, including this one. There are several changes:

  • Slackalaxy has its own domain and there are no advertisements.
  • After this poll at LQ, I gave the Gallery maintenance to Skaendo, a LQ user and maintainer at SBo. I believe he will take a good care of the collection and the SlackBuild.
  • The Biology page was modified, so there are links not only to the projects web-sites but also to relevant entries at SBo.

Well… that’s it, I guess.


Github download links

As a maintainer at SBo, a thing that frequently makes me want to pull my hair off is providing a proper download link for sources hosted at Github. I really should not list all the issues that I have had, because I will get angry. So, straight to the point. Read the rest of this entry »