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/*
* I updated to Ubiquity 0.5 but found that broke
* Julien Couvreur's set-proxy command:
* http://blog.monstuff.com/archives/000342.html.
* So here is a re-write for the new parser.
*/
 
CmdUtils.CreateCommand({
  names: ["set proxy", "proxy", "setproxy"],
  description: "Switch you proxy without going through the preferences menu",

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/*
* This is a command to use the very cool NameLink API provided by the
* Encyclopedia of Life for adding links to biodiversity databases for
* any taxonomic names in a webpage:
* http://hickory.eol.org:8081/display/public/NameLink+Documentation
*/
 
CmdUtils.CreateCommand({
  names: ["taxonomise", "taxonomy", "tax-links"],
  icon: "http://www.gbif.org/favicon.ico",

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# -*- coding: utf-8 -*-
import random

class Lineage:
  """ Model one independantly evolving lineage """
  def __init__(self, complexity= 0, min = None):
    self.complexity = complexity
    self.min = min
  
  def __repr__(self):

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class ORFFinder:
  """Find the longest ORF in a given sequence 
  
   "seq" is a string, if "start" is not provided any codon can be the start of 
   and ORF. If muliple ORFs have the longest length the first one encountered
   is printed 
   """
  def __init__(self, seq, start=[], stop=["TAG", "TAA", "TGA"]):
    self.seq = seq
    self.start = start

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# -*- coding: utf-8 -*-
import random

def round(switch=True):
  doors = ['car', 'goat', 'goat']
  pick = random.randrange(3)
  print "the RNG picked door %s" % (pick + 1)
  #monty knows where the car is
  car = doors.index('car')
  #and he opens a door without the car

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"""
Code writted to answer this challenge at Biostar:
http://biostar.stackexchange.com/questions/5902/

(This code includes improvements from Brad Chapman)
"""

class ORFFinder:
    """Find the longest ORF in a given sequence
    "seq" is a string, if "start" is not provided any codon can be the start of

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"""
Code written to answer stackoverflow question on substitution matrices:
http://stackoverflow.com/questions/5686211/
"""

from Bio.SubsMat import MatrixInfo

def score_match(pair, matrix):
    """ 
    Return score for a given pair of residues in a give matrix.

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import numpy as np
from scipy import cluster
from matplotlib import pyplot

#fake some data
tests = np.reshape( np.random.uniform(0,100,60), (30,2) )

#plot remaining variance for each value for 'k' between 1,10
initial = [cluster.vq.kmeans(tests,i) for i in range(1,10)]
pyplot.plot([var for (cent,var) in initial])

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from Bio import Entrez

#Let NCBI know who you are in case you do something stupid :)
Entrez.email = '[email protected]'

search_s ='"ectomycorrhizal root tip" AND "New Zealand"'
handle = Entrez.esearch(db='nucleotide', term=search_s, retmax=100)
ids = Entrez.read(handle)['IdList']

ids[:5]