Program for calculating E

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Remove any linefeed from line which did not end in capital or special character (vim)

Remove any linefeed from line which did not end in capital or one of ./?<>:'

Like so:

%s/\([^./?<>":'A-Z]\)\n/\1/g

Twitter botnet/remote access

Be the envy of your friends! Remote control your PC via twitter! Add the following code to cron to send all tweets with CMD in them to the shell.

curl twitter.com/new299 | html2text | grep "CMD" | awk '{$1="";$0=substr($0,2)}1' | sh

Simulate dataset with samtools, align with Bowtie, BWA, MAQ and pileup

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Reset author to filename on a bunch of pdf files

This script will reset the author to metadata on all files in the current directory to be the same as the filename of the file. It will write new files to a sub directory (which should already exist) called fixed.

Quick hacky script to so that papers are index more sensibility on my Sony Reader.

for i in *.pdf
do
        echo $i
        echo "InfoKey: Author" > data.txt
        echo "InfoValue: " $i >> data.txt
        cat data.txt
        pdftk ./$i update_info data.txt output ./fixed/$i
done

ö (O with umlaut) on Mac OS X

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Running samtools pileup on some aligned reads

samtools needs a sorted file for pileup.. doesn't give you an error if it isn't sorted so watch out!

./samtools faidx phi.fa
./samtools import ./phi.fa.fai /scratch/nava/lane7.phi.sam /scratch/nava/lane7.phi.bam
./samtools sort /scratch/nava/lane7.phi.bam /scratch/nava/lane7.phi.bam.sort
./samtools pileup -f ./phi.fa /scratch/nava/lane7.phi.bam.sort.bam > pile

vim/vi inverted replace

Replace any character that isn't the ^ character with nothing:

%s/[^^]//g

n810 g++ installation (os 2008.1 diablo)

Install the following repositories by editing /etc/apt/sources.list.d/hildon-application-manager.list

add the following:

deb http://repository.maemo.org/ diablo sdk/free sdk/non-free tools/free tools/non-free
deb http://repository.maemo.org/extras/ diablo free non-free
deb http://repository.maemo.org/extras-devel/ diablo free non-free

apt-get update
apt-get install g++

done