Tag Archive for 'linux'

Count the number of sequences in a FASTA format file: a Unix shell snippet

Published
by
perry
on September 1, 2008
in bioinformatics, linux and software
. 4 Comments

Sometimes it’s nice to quickly check how many sequences are in a FASTA format sequence file.

It barely warrants it’s own blog post, but here we go anyhow: my one-liner shell script for counting the number of sequences in a FASTA “flat-file database”, based on the presence of the “>” header symbol.

#!/bin/sh
# ~/bin/countseqs
# Counts the number of sequences in a FASTA format file
grep ">" $1 | wc -l

Dead easy huh ? I put this in ~/bin/countseqs, make it executable (chmod +x ~/bin/countseqs) and use it in lots of situations, as a quick sanity check.

(oh, btw, this is not public domain and u can’t use it for commercial gain without paying me a license fee. academic users can fax me something for a free license. k thx bye).

Couldn’t help myself … everyone else is doing it :)

Setting up NCBI wwwblast on Ubuntu 8.04 (Hardy), Apache 2

Published
by
perry
on August 25, 2008
in bioinformatics and linux
. 7 Comments

Recently I needed to install NCBI wwwblast on my local workstation to enable some software that needed to interface with BLAST via the web service. It was straightforward to install, but I took some notes, because there were a few changes required with respect to the official wwwblast documentation at NCBI. These instructions are for Ubuntu 8.04, but probably will work with many recent flavours of Debian.
Continue reading ‘Setting up NCBI wwwblast on Ubuntu 8.04 (Hardy), Apache 2′