andrewdyates

#!/usr/bin/python2.5
# -*- coding: utf-8 -*-
# Copyright © 2010 Andrew D. Yates
# All Rights Reserved
"""Assorted Google App Engine Python Utilities.

ID: random string for IDs
KeyPath: human readable path of an app engine datastore key
Cookie: generate HTTP cookie header formatted string 
"""

andrewdyates

<samlp:Response xmlns:saml="urn:oasis:names:tc:SAML:2.0:assertion" xmlns:samlp="urn:oasis:names:tc:SAML:2.0:protocol" ID="{{ response_id }}" IssueInstant="{{ issue_instant }}" Version="2.0"><samlp:Status><samlp:StatusCode Value="urn:oasis:names:tc:SAML:2.0:status:Success"></samlp:StatusCode></samlp:Status><saml:Assertion ID="{{ assertion_id }}" IssueInstant="{{ issue_instant }}" Version="2.0"><saml:Issuer>{{ issuer }}</saml:Issuer><saml:Subject><saml:NameID Format="urn:oasis:names:tc:SAML:1.1:nameid-format:emailAddress">{{ username }}</saml:NameID><saml:SubjectConfirmation Method="urn:oasis:names:tc:SAML:2.0:cm:bearer"><saml:SubjectConfirmationData {% if request_id %}InResponseTo="{{ request_id }}" {% endif %}NotOnOrAfter="{{ not_on_or_after }}" Recipient="{{ acs_url }}"></saml:SubjectConfirmationData></saml:SubjectConfirmation></saml:Subject><saml:Conditions NotBefore="{{ not_before }}" NotOnOrAfter="{{ not_on_or_after }}"><saml:AudienceRestriction><saml:Audience>{{ acs_url }}</saml:Audience></saml:AudienceR

andrewdyates

application: myapplication
version: 1
runtime: python
api_version: 1

handlers:

- url: /_ah/login_required
  script: do_openid_login.py

andrewdyates

import gzip
import zipfile

def open_with_zip(filepath):
  """Open a file with .gzip, .zip, or no compression.

  Returns:
    [*str] read filepointer of uncompressed file stream
  """
  ext = filepath.lower().rpartition('.')[-1]

andrewdyates

# -*- coding: utf-8 -*-
"""

Created on Fri Jun 15 14:00:29 2012

Author: Josef Perktold
License: MIT, BSD-3 (for statsmodels)

http://en.wikipedia.org/wiki/Distance_correlation
Yaroslav and Satrajit on sklearn mailing list

andrewdyates

# Copyright (c) 2012, Florian Finkernagel. All right reserved.
## Redistribution and use in source and binary forms, with or without
## modification, are permitted provided that the following conditions are
## met:

##     * Redistributions of source code must retain the above copyright
##       notice, this list of conditions and the following disclaimer.

##     * Redistributions in binary form must reproduce the above
##       copyright notice, this list of conditions and the following

andrewdyates

#!/usr/bin/python
import numpy as np
import os

TEST_FILE=os.path.expanduser("~/Dropbox/biostat/eqtl_data/GSE25935/GSE25935.GPL4133.eQTL.nooutliers.tab")

# this does not (yet) work
# http://docs.scipy.org/doc/numpy/reference/generated/numpy.genfromtxt.html#numpy.genfromtxt
# http://docs.scipy.org/doc/numpy/reference/generated/numpy.loadtxt.html#numpy.loadtxt

andrewdyates

"""
=====================================================
Distance computations for masked arrays (:mod:`scipy.spatial.mdistance`)
=====================================================

.. sectionauthor:: Damian Eads, Jason Merkin

Function Reference
------------------

andrewdyates

# http://stackoverflow.com/questions/842059/is-there-a-portable-way-to-get-the-current-username-in-python
import os, pwd
username = pwd.getpwuid(os.getuid()).pw_name

andrewdyates

#!/usr/bin/python
import os, errno

def make_dir(outdir):
  try:
    os.makedirs(outdir)
  except OSError, e:
    if e.errno != errno.EEXIST: raise
  return outdir