terrycojones

#!/usr/bin/env python

import sys

seen = {}

for lineNumber, line in enumerate(sys.stdin):
    if lineNumber:
        fields = line.split('|')
        key = '|'.join(fields[:2] + fields[3:])

terrycojones

#!/usr/bin/env python

import sys
from collections import defaultdict

seen = defaultdict(list)

for lineNumber, line in enumerate(sys.stdin):
    if lineNumber:
        fields = line.split('|')

terrycojones

Subjects (with offsets) by hash:
   GB7:GA24:87
    gi|285002301|ref|YP_003422365.1| envelope fusion protein [Pseudaletia unipuncta granulovirus] [453]
    gi|311977556|ref|YP_003986676.1| hypothetical protein [Acanthamoeba polyphaga mimivirus] [88]
    gi|9626461|ref|NP_059434.1| hypothetical protein JEVgp1 [Japanese encephalitis virus] [3118]
    gi|20564197|ref|NP_620735.1| replication-associated protein [Tomato pseudo-curly top virus] [228]
    gi|448825870|ref|YP_007418801.1| putative ankyrin repeat protein [Megavirus lba] [153]
    gi|226377796|ref|YP_002790845.1| hypothetical protein lb338_phage_166 [Lactobacillus phage Lb338-1] [97]
    gi|563397262|ref|YP_008857028.1| putative DNA ligase [Pseudomonas phage PAK_P5] [117]
    gi|118197773|ref|YP_874166.1| hypothetical protein YS40_153 [Thermus phage phiYS40] [539]

terrycojones

from collections import defaultdict

def confusion(trueLabels, clusterLabels):
    counts = defaultdict(lambda: defaultdict(int))
    allLabels = sorted(set(trueLabels + clusterLabels))
    for trueLabel, clusterLabel in zip(trueLabels, clusterLabels):
        counts[trueLabel][clusterLabel] += 1
    return allLabels, counts

terrycojones

from collections import Counter, defaultdict

class ConfusionMatrix(object):
    def __init__(self, trueLabels, clusterLabels):
        self._counts = defaultdict(Counter)
        self.allLabels = set(trueLabels + clusterLabels)
        for trueLabel, clusterLabel in zip(trueLabels, clusterLabels):
            self._counts[trueLabel][clusterLabel] += 1
        
    def __getitem__(self, item):

terrycojones

    def checkAlphabet(self, count=10):
        """
        """
        alphabet = Read.checkAlphabet(self, count)
        if len(self) > 10 and alphabet.issubset(set('ACGT')):
            raise ...

# using the new-style classes super():

    def checkAlphabet(self, count=10):

terrycojones

#!/bin/bash

# A Git pre-commit hook.
#
# To install:
#
#   $ cd .git/hooks
#   $ ln -s ../../bin/pre-commit.sh pre-commit

# Add our virtualenv bin to PATH. Git commit seems to muck with PATH :-(

terrycojones

var wsuri = "ws://127.0.0.1:8080/ws";

var connection = new autobahn.Connection({
	url: wsuri,
	realm: "realm1",
	use_deferred: jQuery.Deferred
});

var jqueryReady = jQuery.Deferred();
var routerReady = jQuery.Deferred();

terrycojones

$ ls -la /usr/local/bin/gcc*
lrwxr-xr-x  1 terry  admin   7 Aug  6  2014 /usr/local/bin/gcc -> gcc-4.9
lrwxr-xr-x  1 terry  admin  46 Sep 21  2014 /usr/local/bin/gcc-4.2 -> ../Cellar/apple-gcc42/4.2.1-5666.3/bin/gcc-4.2
lrwxr-xr-x  1 terry  admin  33 Jan 14 10:04 /usr/local/bin/gcc-4.9 -> ../Cellar/gcc/4.9.2_1/bin/gcc-4.9
lrwxr-xr-x  1 terry  admin  36 Jan 14 10:04 /usr/local/bin/gcc-ar-4.9 -> ../Cellar/gcc/4.9.2_1/bin/gcc-ar-4.9
lrwxr-xr-x  1 terry  admin  36 Jan 14 10:04 /usr/local/bin/gcc-nm-4.9 -> ../Cellar/gcc/4.9.2_1/bin/gcc-nm-4.9
lrwxr-xr-x  1 terry  admin  40 Jan 14 10:04 /usr/local/bin/gcc-ranlib-4.9 -> ../Cellar/gcc/4.9.2_1/bin/gcc-ranlib-4.9

terrycojones

Bayes is cool!

From the introduction to An Intuitive Explanation of Bayes' Theorem:

Your friends and colleagues are talking about something called "Bayes' Theorem" or "Bayes' Rule", or something called Bayesian reasoning. They sound really enthusiastic about it, too, so you google and find a webpage about Bayes' Theorem and... >