dansondergaard

int *translate_observations_to_indexes(struct hmm_t *hmm, const char *observations) {
  int *observations_idx = malloc(strlen(observations) * sizeof(int));
  for (int i = 0; i < strlen(observations); i++) {
    for (int j = 0; j < hmm->observables_size; j++) {
      if (observations[i] == hmm->observables[j]) {
        observations_idx[i] = j;
      }
    }
  }
  return observations_idx;

dansondergaard

class Node(object):
    def __init__(self, name, checkpoint=False):
        self.name = name
        self.explored = False
        self.checkpoint = checkpoint
        self.edges = []

    def add_edge(self, other):
        self.edges.append(other)

dansondergaard

class Logger(object):
    def __init__(self):
        self.records = []
    def write(self, record):
        self.records.append(record)

logger = Logger()

print >> logger, "hello"
print >> logger, "world"

dansondergaard

# naivebayes.txt
#
# sex height weight  footsize
# male  6    180	12
# male	5.92 190	11
# male	5.58	170	12
# male	5.92	165	10
# female 5	100	6
# female 5.5	150	8
# female 5.42	130	7

dansondergaard

"""Decision Tree"""

__all__ = ['grow', 'classify']


class Node(object):
    def __init__(self, error, dimension, value, left, right):
        self.error = error
        self.dimension = dimension
        self.value = value

dansondergaard

def compute_error(partition):
    """Find the majority category of the partition. Count how big
       a part of the partition that the majority category is.
       Return the ratio of things that are *not* of the majority category."""
    categories = map(get_category, partition)
    majority = max(set(categories), key=categories.count)
    return 1 - (categories.count(majority) / float(len(partition)))

# This is what a typical partition looks like. The inner tuple may
# be very large (in the thousands) and the list of the length may

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class symbol(object):
    _symbols = {}

    def __new__(cls, name):
        if name not in symbol._symbols:
            symbol._symbols[name] = object.__new__(cls, name)
        return symbol._symbols[name]

    def __init__(self, name):
        self.name = name

dansondergaard

import xml.etree.ElementTree as et
import base64
import array


def parse_file(filename_or_obj):
    tree = et.parse(filename_or_obj)
    for spectrum in tree.findall('.//spectrum'):
        mz_elm = spectrum.find('mzArrayBinary').find('data')
        intensity_elm = spectrum.find('intenArrayBinary').find('data')

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#!/usr/bin/env python3

import sys
import os
import os.path
import argparse

import subprocess

DEVNULL = open(os.devnull, 'wb')

dansondergaard

#################
# notifications #
#################

function __record_cmd_begin -d "Record time when command started." -e fish_preexec
  set -g cmd_begin_time (eval date +"%s")
end

function __record_cmd_end -d "Record time when command ended." -e fish_postexec
  set -g cmd_end_time (eval date +"%s")