Samuel Lampa samuell

💻

Hacking away

Bioinformatician in clinical microbiology. Occasionally hacking on stuff like @flowbase, @scipipe & @rdfio

samuell / Snakefile

Created February 25, 2015 15:23

Testing some stuff with snakemake ...

	rule rawdata:
	output: '{base}.raw.fa'
	shell: 'echo "ACGTTGCA" > {output}'

	rule atot:
	input: '{base}.fa'
	output: '{base}.atot.fa'
	shell: 'cat {input} \| sed "s/A/T/g" > {output}'

	rule ctog:

samuell / pipes_to_subprocess.py

Created February 16, 2015 21:56

Parse a shell command with pipe characters, into a subprocess chain

	import subprocess as sub

	def create_pipes(cmd):
	procs = {}
	parts = cmd.split('\|')
	for i, part in enumerate(parts):
	cmdparts = part.strip().split(' ')

	if i == 0:
	procs[i] = sub.Popen(cmdparts, stdout=sub.PIPE)

samuell / reseqtut_lmw.py

Last active October 3, 2016 12:29

Some steps from the the Re-sequencing NGS intro tutorial [1], using Luigi workflow system [2] with the Luigi's Monkey Wrench [3] wrapper. (Refs: [1]: http://uppnex.se/twiki/do/view/Courses/NgsIntro1502/ResequencingAnalysis.html [2]: https://github.com/spotify/luigi [3]: https://github.com/samuell/luigis_monkey_wrench )

	import luigi
	from luigis_monkey_wrench import *

	REF='human_17_v37.fasta'
	INDIVIDUALS=['NA06984','NA07000']
	SAMPLES=['1','2']
	BASENAME='.ILLUMINA.low_coverage.17q_'
	PICARDDIR='/sw/apps/bioinfo/picard/1.69/kalkyl/'
	KNOWNSITES='/proj/g2014207/labs/gatk/ALL.chr17.phase1_integrated_calls.20101123.snps_indels_svs.genotypes.vcf'

samuell / pgsql_cheatsheet.sql

Created October 9, 2014 10:02

	# change to postgres user and open psql prompt
	sudo -u postgres psql postgres

	# list databases
	postgres=# \l

	# list roles
	postgres=# \du

	# create role

samuell / MANIFEST.MF

Created October 7, 2014 16:07

Example of a minimal META-INF/MANIFEST.MF file for creating jar files

samuell / zoom_xfce4_terminal.sh

Created October 3, 2014 14:51

Place this in your ```~/.bash_aliases``` file.

	zi() {
	if [[ ! -z $1 ]]; then
	steps=$1;
	SIZE=`grep 'FontName' ~/.config/Terminal/terminalrc \| cut -d' ' -f 2`
	NEWSIZE=$((SIZE + steps))
	REGEXPR='s/FontName.*/FontName=Monospace '$NEWSIZE'/g'
	sed -i "$REGEXPR" ~/.config/Terminal/terminalrc
	else
	echo "Usage: zi [zoom steps]";
	fi;

samuell / gc_ratio_calc.exs

Created September 30, 2014 14:49

	defmodule ATGCCount do
	def count(sequence), do: cnt(String.to_char_list(sequence),0,0)
	def cnt([65\|t],at,gc), do: cnt(t,at+1,gc)
	def cnt([84\|t],at,gc), do: cnt(t,at+1,gc)
	def cnt([71\|t],at,gc), do: cnt(t,at,gc+1)
	def cnt([67\|t],at,gc), do: cnt(t,at,gc+1)
	def cnt([62\|_],at,gc), do: {at,gc}
	def cnt([],at,gc), do: {at,gc}
	def cnt(_,0,0), do: {0,0}
	def cnt([_\|t], at, gc), do: cnt(t,at,gc)

samuell / essential.vimrc

Last active August 29, 2015 14:06

	inoremap jj <ESC>

	noremap <silent> <c-z> :update<CR>
	inoremap <silent> <c-z> <c-[>:update<CR>
	vnoremap <silent> <c-z> :<c-c>:update<CR>

	noremap <c-j> 4j
	noremap <c-k> 4k
	noremap <c-h> 4h
	noremap <c-l> 4l

samuell / essential_aliases.sh

Last active August 29, 2015 14:06

samuell / install_irods_deb.log.sh

Last active October 7, 2016 04:16

	[xubuntu ~/install/irods]$ l
	irods-database-plugin-postgres-1.3.deb
	irods-icat-4.0.3-64bit.deb
	[xubuntu ~/install/irods]$ sudo dpkg -i *.deb
	[sudo] password for xubuntu:
	Selecting previously unselected package irods-database-plugin-postgres.
	(Reading database ... 179210 files and directories currently installed.)
	Preparing to unpack irods-database-plugin-postgres-1.3.deb ...
	Unpacking irods-database-plugin-postgres (1.3) ...
	Selecting previously unselected package irods-icat.

	defmodule ATGCCount do
	def count(sequence), do: cnt(String.to_char_list(sequence),0,0)
	def cnt([65\|t],at,gc), do: cnt(t,at+1,gc)
	def cnt([84\|t],at,gc), do: cnt(t,at+1,gc)
	def cnt([71\|t],at,gc), do: cnt(t,at,gc+1)
	def cnt([67\|t],at,gc), do: cnt(t,at,gc+1)
	def cnt([62\|_],at,gc), do: {at,gc}
	def cnt([],at,gc), do: {at,gc}
	def cnt(_,0,0), do: {0,0}
	def cnt([_\|t], at, gc), do: cnt(t,at,gc)