armanbilge

#!/usr/bin/env python

import sys
from dendropy import TreeList

NEWICK = 'newick'
NEXUS = 'nexus'

try:
    stream = sys.argv[1]

armanbilge

#!/usr/bin/env python
# FlickrSetDownloadr.py
# Downloads photos from a Flickr set
# Usage: python FlickrSetDownloadr.py [PHOTOSET_ID]

import sys
from collections import deque
try:
    from xml.etree.cElementTree import fromstring
except:

armanbilge

#!/usr/bin/env python
# SecretSnowflakeOrganizer.py
# Web app that automatically coordinates a Secret Snowflake Gift Exchange

COORDINATOR_PASSWORD = 'COORDINATOR_PASSWORD'
DB_HOST = 'DB_HOST'
DB_USER = 'DB_USER'
DB_PASSWORD = 'DB_PASSWORD'
DB_NAME = 'DB_NAME'
GMAIL_USER = 'EMAIL'

armanbilge

import sys; print '\n'.join([l.split(',')[0] + '\t' + l.split(',')[-5] for l in open(sys.argv[1])]);

armanbilge

#!/usr/bin/env python3

import sys
from fractions import Fraction

mult = lambda r,f: [f * x for x in r]
add = lambda r1,r2: [x + y for x,y in zip(r1,r2)]

def print_matrix(m):
    for r in m: print('\t'.join(str(x) for x in r))

armanbilge

#!/usr/bin/python
 
import smtplib
from email.MIMEMultipart import MIMEMultipart
from email.MIMEBase import MIMEBase
from email.MIMEText import MIMEText
from email import Encoders
import os
 
gmail_user = "[email protected]"

armanbilge

next_poisson <- function(lambdas) {
    lambda <- sum(lambdas)
    t <- rexp(1, rate = lambda)
    i <- sample(length(lambdas), 1, prob = lambdas / lambda)
    return(c(t, i))
}

duplication <- function(s) {
    i <- sample(length(s), 1, prob = s / sum(s))
    s[i] <- s[i] + 1

armanbilge

\documentclass[11pt]{article}
\usepackage[margin=1in]{geometry}

\usepackage{amsmath}

\frenchspacing

\begin{document}

\begin{tabular}{l c l}

armanbilge

from string import ascii_lowercase as alphabet
f = lambda i: alphabet[i] if i < 26 else alphabet[i / 26 - 1] + alphabet[i % 26]

armanbilge

    public static void main(String... args) throws IOException, Importer.ImportException {
        final TreeModel tree = new TreeModel(new NewickImporter("(a:1,b:1);").importNextTree());
        final SimpleAlignment alignment = new SimpleAlignment();
        alignment.setDataType(Nucleotides.INSTANCE);
        alignment.addSequence(new Sequence(new Taxon("a"), "A"));
        alignment.addSequence(new Sequence(new Taxon("b"), "C"));
        final PatternList patterns = new SitePatterns(alignment);
        final SiteModel siteModel = new GammaSiteModel(new GTR(new Variable.D(1, 1), new Variable.D(1, 1), new Variable.D(1, 1), new Variable.D(1, 1), new Variable.D(1, 1), new Variable.D(1, 1), new FrequencyModel(Nucleotides.INSTANCE, new double[]{0.25, 0.25, 0.25, 0.25})));
        final TreeLikelihood likelihood = new TreeLikelihood(patterns, tree, siteModel, new DefaultBranchRateModel(), null, true, false, true, true, false);
        final Variable<Double> var = tree.createNodeHeightsParameter(true, true, false