buchanae

# This is my preferred way to use print
# and makes my code compatible with future versions
# of python.  More info here:
# http://docs.python.org/2/library/functions.html#print
from __future__ import print_function 

# http://docs.python.org/2/library/functions.html#open
# http://effbot.org/zone/python-with-statement.htm
with open('output.txt', 'w') as file_handle:
    # notice I didn't add a newline at the end, print() does that for you

buchanae

from __future__ import print_function

# The tree:
#        a
#    b       c
#  d   e   f   g
# h i j k l m n o

graph = {
    'a': ['b', 'c'],

buchanae

from collections import defaultdict

def splitter(lines, keyfunc, valuefunc):
    d = defaultdict(list)

    for line in lines:
        cols = line.split()
        key = keyfunc(cols)
        value = valuefunc(cols)
        d[key].append(value)

buchanae

# maps names to OTU numbers
name_to_OTU = {
    'name_1': 23,
    'RIO12.3_44008': 93,
}

# contrived data to represent what you emailed
# this represents one sample's counts,
# e.g. the "('MID - OLD12.5',..." line
per_sample_counts = Counter({

buchanae

from collections import namedtuple
import jsonpickle

Foo = namedtuple('Foo', 'bar')

foo = Foo('bar')

encoded = jsonpickle.encode(foo)
decoded = jsonpickle.decode(encoded)
assert isinstance(decoded, Foo), 'decoded has type {}'.format(type(decoded))

buchanae

from __future__ import print_function


otu_list = ['otu1', 'otu2', 'otu15']
d = {'nice name': {'otu1': 24, 'otu15': 57}}

for name, otu_counts in d.items():
    cols = []
    for otu_key in otu_list:
        count = otu_counts.get(otu_key, 0)

buchanae

(jeans)jeans$ pip install pysam
Downloading/unpacking pysam
  Downloading pysam-0.7.4.tar.gz (1.4MB): 1.4MB downloaded
  Running setup.py egg_info for package pysam
    Downloading http://pypi.python.org/packages/source/d/distribute/distribute-0.6.34.tar.gz
    Extracting in /var/folders/vU/vURgXIhFG6O8EVY7ATHbn++++TQ/-Tmp-/tmpE5Lp4T
    Now working in /var/folders/vU/vURgXIhFG6O8EVY7ATHbn++++TQ/-Tmp-/tmpE5Lp4T/distribute-0.6.34
    Building a Distribute egg in /Users/abuchanan/.virtualenvs/jeans/build/pysam
    /Users/abuchanan/.virtualenvs/jeans/build/pysam/distribute-0.6.34-py2.7.egg
    /usr/local/Cellar/python/2.7.3/Frameworks/Python.framework/Versions/2.7/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'use_2to3'

buchanae

import string


class FormatKeyError(Exception):
    def __init__(self, key):
        self.key = key


class OptionalFormatter(string.Formatter):

buchanae

def get_class(name):
    # Reflection: try to get the exception class

    # Try to split the name on dots,
    # in case it contains a module path
    parts = name.split('.')

    if len(parts) == 1:
        # If it didn't have a module path,

buchanae

class Album(Model):
    ...

class Track(Model):
    album = ForeignKey(Album)

class AlbumSerializer(HyperlinkedModelSerializer):
    ...

class TrackTest(APITestCase):