konrad

import argparse
from Bio import SeqIO

parser = argparse.ArgumentParser(
    description="Split a multi entry fasta file into several files "
    "with one entry")
parser.add_argument("input_file")
parser.add_argument("output_prefix")
args = parser.parse_args()

konrad

# Search for all mp3 and ogg files in my music folder and use mplayer to play in random order
mplayer -shuffle -playlist $(find $MY_MUSIC_FOLDER -name "*ogg" -o -name "*mp3")

konrad

#!/usr/bin/python 

# medline_search.py
#
# Small script to retrieve data of all publications of a given journal in
# a given time frame from MEDLINE
#
# 2014 - Konrad Förstner <[email protected]>
#
#  To the extent possible under law, the author have dedicated all

konrad

main(){
    upgrade_and_install_packages
    install_segemehl
    install_reademption
}

upgrade_and_install_packages(){
    sudo apt-get update
    sudo apt-get upgrade --assume-yes
    sudo apt-get install --assume-yes \

konrad

#!/usr/bin/env python
"""
FUNCTION: Converts a CSV (tab delimited) file to an Excel xlsx file.

Copyright (c) 2016, Konrad Foerstner <[email protected]>

Permission to use, copy, modify, and/or distribute this software for
any purpose with or without fee is hereby granted, provided that the
above copyright notice and this permission notice appear in all
copies.

konrad

SPEED=1.5

for FILE in $@
do
    WAV_FILE=$(basename $FILE .mp4).wav
    WAV_FILE_SPED_UP=$(basename $FILE .mp4)_spedup.wav
    MP3_FILE=$(basename $FILE .mp4)_spedup.mp3
    ffmpeg -i $FILE -vn $WAV_FILE
    sox $WAV_FILE $WAV_FILE_SPED_UP tempo $SPEED
    lame $WAV_FILE_SPED_UP $MP3_FILE

konrad

/*
Use this as a bookmarklet by saving it as a web browser bookmark. Then mark a piece of text in a page and click the bookmark. The marked text will be searched in Pubmed.
*/

javascript:(function(){
    var selected_text = '';
    if (window.getSelection){
        selected_text = window.getSelection();
    }
    else if (document.getSelection){

konrad

import sys

base_seq = "ACGT"
seq = base_seq * int(int(sys.argv[1])/len(base_seq))
spacer_length = 10000
header = "@HD	VN:1.0\n@SQ	SN:Mock	LN:%s" % (len(seq) + spacer_length)

cigar_string = "%sM" % (len(seq))
genome_line = "62DJLAAXX_8:1:17056:1190	0	Mock	1	255	%s	*	0	0	%s	*	NM:i:0	MD:Z:30	NH:i:1" % (
    cigar_string, seq)

konrad

# I always forget how easy it is to download all genome files from 
# Genbank. Sure you can get any other file type (e.g. all  protein 
# file = *faa) instead.
wget -c -r -A "*fna" ftp://ftp.ncbi.nih.gov/genomes/Bacteria/

konrad

#!/usr/bin/python                                                                          

"""                                                                                        
FUNCTION: A little example how to send messages to a OneSociaWeb server                      
          (http://onesocialweb.org). Heavily inspired by Tyler                             
          Gillies' ruby script with the same purpose.                                      
                                                                                           
Copyright (c) 2010, Konrad Foerstner <[email protected]>                                
                                                                                           
Permission to use, copy, modify, and/or distribute this software for