armanbilge

#!/usr/bin/env python3

import sys
from Bio import SeqIO

for fn in sys.argv[1:]:
    with open(fn, 'r') as f:
        print('\t<data id="{}" name="alignment">'.format(fn[:-len('_unphased.nex')]))
        for record in SeqIO.parse(f, 'nexus'):
            if record.id.endswith('_1'):

armanbilge

#!/usr/bin/env ruby
Encoding.default_external = "UTF-8"

i = 0
puts STDIN.read.sub(/(WEBVTT\s+)(\d{2}:)/){|s| "#{$2}"}.gsub(/(\d{2}:\d{2})\.(\d{3}\s+)-->(\s+\d{2}:\d{2})\.(\d{3}\s*)/) { |s|
  "#{i+=1}\n#{s.sub(/(\d{2}:\d{2})\.(\d{3}\s+)-->(\s+)(\d{2}:\d{2})\.(\d{3}\s*)/){|t| "00:#{$1},#{$2}-->#{$3}00:#{$4},#{$5}"}}"
}

armanbilge

import string
from collections import Counter

def leastFrequentLetters(s):
    C = Counter(c for c in s.lower() if c in string.ascii_lowercase)
    return ''.join(k for k in string.ascii_lowercase if C[k] == min(C.itervalues()))

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

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

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

\usepackage{amsmath}

\frenchspacing

\begin{document}

\begin{tabular}{l c l}

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

#!/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

#!/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

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