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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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 »


Ratiometric flow cytometry plot

I decided to make a ratiometric flow cytoetry analysis in FCSalyzer, since the program is free, cross-platform and easy to use (also, I just like it a lot). Such feature, however, has not been implemented yet, but is in the to-do list of the developer, Dr. Sven Mostböck. As a workaround, I used two small programs from the same author: FCS2Data and Data2FCS. Read the rest of this entry »


Cleaning up with sed

I needed to clean up some plain text files from data and characters I did not want.

To be more precise, I have a phylogenetic tree, obtained from the TimeTree web-site. Species presented there are mainly birds, several reptiles and a fish. The tree has branches length information and node labels, which I wanted to remove.
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