lomereiter

# -*- coding: utf-8 -*-
Rule = Struct.new :from, :to, :exit

def parseSingleRule(rule_src)
  rule_src =~ /^\s*([^\s]*)\s*=>\s*([\.]?)([^\s]*)\s*$/
  r = Rule.new($1, $3)
  r.exit = $2 == '.'
  r
end

lomereiter

import bio.bam.reader;
import bio.bam.pileup;

import bio.core.base;
import bio.core.tinymap;

import std.stdio, std.parallelism, std.algorithm, std.array, std.range;

void main(string[] args) {
    defaultPoolThreads = 4;

lomereiter

import std.stdio, std.range, std.algorithm, std.conv, std.string, std.file;

immutable letters = "abcdefghijklmnopqrstuvwxyz"d;

auto replaces(S)(S word) {
  return word.length.iota.map!(i =>
           letters.length.iota.map!(j =>
             word[0 .. i].chain(letters[j .. j+1], word[i+1 .. $])))
         .joiner;
}

lomereiter

// building suffix trees in linear time using the Ukkonen's algorithm
//
// with -debug flag, LOTS of output is printed during construction
// so that each step of the algorithm can be studied

import std.stdio;
import std.array, std.range, std.algorithm;

class SuffixTree {
  static struct Node {

lomereiter

import cv
import commands
import time
from PIL import Image
from collections import deque

camera = cv.CreateCameraCapture(-1)

prev_brightness_values = deque([], 5)
prev_brighness = None

lomereiter

> git-lfs smudge genotype_files/gemma/HLC.map
LocalWorkingDir=/home/lomereiter/github/genenetwork2
LocalGitDir=/home/lomereiter/github/genenetwork2/.git
LocalMediaDir=/home/lomereiter/github/genenetwork2/.git/lfs/objects
TempDir=/home/lomereiter/github/genenetwork2/.git/lfs/tmp
GIT_DIR=.git

Error accessing media: genotype_files/gemma/HLC.map (84241b81feb7eec3c0b914e223ff23810c69610a6e759baf4797bab4a4850de8)

Error downloading /home/lomereiter/github/genenetwork2/.git/lfs/objects/84/24/84241b81feb7eec3c0b914e223ff23810c69610a6e759baf4797bab4a4850de8.

lomereiter

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index a572a60..b152357 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -555,12 +555,22 @@ class DataSet(object):
         #  """ % (query_args))
         
         try:
-            self.id, self.name, self.fullname, self.shortname = g.db.execute("""
+            if self.type != "ProbeSet":

lomereiter

// compilation: rdmd --build-only -O -release -inline -IBioD sambamba_161.d
// to use LDC: rdmd --compiler=ldmd2 [--force] ...
import bio.bam.reader, bio.bam.writer, std.parallelism;

void main(string[] args) {
  // boilerplate
  defaultPoolThreads = 8;
  auto input = new BamReader(args[1]); // use std.getopt for better args handling
  auto output = new BamWriter(args[2]);
  output.writeSamHeader(input.header);

lomereiter

import sys
# path to pyIMS parent dir
sys.path.append("/home/lomereiter/github")

from pyIMS.image_measures.level_sets_measure import measure_of_chaos
from pyIMS.image_measures.isotope_image_correlation import isotope_image_correlation
from pyIMS.image_measures.isotope_pattern_match import isotope_pattern_match

import numpy as np
import cPickle

lomereiter