Samuel Lampa samuell

💻

Hacking away

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

samuell / reproduce_arc2_turtleparser_bug.php

Created October 18, 2013 11:58

	<?php

	require_once('ARC2.php');

	// Init parser
	$parser = ARC2::getTurtleParser();

	$turtle = <<<EOD

	@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .

samuell / exec_cmd.py

Last active December 27, 2015 09:49

A convenience method for executing external commands and getting the output, in python

	import subprocess as sub

	def exec_cmd(commandstr):
	proc = sub.Popen(commandstr, stdout=sub.PIPE, shell=True)
	return proc.communicate()[0].strip()

samuell / numap_test.py

Last active December 27, 2015 11:28

Spawning parallel jobs with NuMap

	from numap import NuMap
	import time

	def capitalizer(name):
	time.sleep(1)
	return name.capitalize()

	namelist = ('rolf', 'mariann', 'samuel', 'sandra', 'simon', 'theresa', 'jonathan', 'elias', 'miryam')

	result_iterator = NuMap(capitalizer, namelist)

samuell / basecompl_papy.py

Created November 7, 2013 16:14

Base complementer example in Papy, trying to add multple workers in to a single piper

	__author__ = 'samuel'

	from papy.core import Worker, Plumber, Piper
	from papy.core import start_logger
	from numap import NuMap

	infile_name = "Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa.short"

	def base_complement( inbox ):
	def basecompl_nucl(nucl):

samuell / basecompl_papy.py

Created November 7, 2013 16:18

Base complementer example in PaPy

	__author__ = 'samuel'

	from papy.core import Worker, Plumber, Piper
	from papy.core import start_logger
	from numap import NuMap

	infile_name = "Homo_sapiens.GRCh37.67.dna_rm.chromosome.Y.fa.short"

	def base_complement( inbox ):
	def basecompl_nucl(nucl):

samuell / basic_luigi_cli_task.py

Last active December 27, 2015 18:39

	class ATask(luigi.Task):

	def requires(self):
	# Defines what is the upstream task to this one.
	# Is later used by the input() function.
	return APreviousTask()

	def output(self):
	return luigi.LocalTarget(self.input().path + ".new_extension")

samuell / stream_editing_tsv.py

Last active December 28, 2015 03:39

Example showing how to manipulate tab separated data on the standard input, and write the manipulated data to standard output.

	import csv
	from sys import stdin, stdout

	tsv_in = csv.reader(stdin, delimiter="\t")
	tsv_out = csv.writer(stdout, delimiter="\t")

	for row in tsv_in:
	# Write out only columns 2-*
	tsv_out.writerow(row[1:])

samuell / select_parent_luigi_task_by_param.py

Created December 3, 2013 18:51

Demonstrates how one can select which parent task a luigi task should depend on, by specifying the parent task class name via a parameter.

	import luigi

	class ATask(luigi.Task):

	def output(self):
	return luigi.LocalTarget("atask_output.txt")

	def run(self):
	with self.output().open("w") as outfile:
	outfile.write("Test")

samuell / luigi_dynamic_dependency_graph_definition.py

Last active March 21, 2020 14:57

Dynamically specify luigi data flow

	import luigi

	class ATask(luigi.Task):

	def output(self):
	return luigi.LocalTarget("atask_output.txt")

	def run(self):
	with self.output().open("w") as outfile:
	outfile.write("Test")

samuell / neat.py

Last active December 31, 2015 01:29

"Neat way to {do_what} in {lang}".format(do_what="format strings", lang="python")﻿