ArtPoon

import random
import argparse


description = """
Random permutation of FASTA file.
This script reads a FASTA-formatted file containing aligned sequences and
applies a random permutation of alignment columns (nucleotide sites),
writing the result to a new FASTA file.  A random permutation changes the
order of a sequence.  For example, (1,2,3,4,5) may become (4,2,1,3,5).

ArtPoon

import sys
import lzma
import os
import csv
import subprocess
import tempfile
from mpi4py import MPI

comm = MPI.COMM_WORLD
my_rank = comm.Get_rank()

ArtPoon

# Let 25,000 be a circle of unit radius (area = pi)
require(ggfree)

png(file="~/Desktop/canada-data-sharing.png", width=5*200, height=5.25*200, res=200)

par(mar=c(1,1,3,1), family='Palatino', bg=rgb(.14, .12, .27), xpd=NA)

plot(NA, xlim=c(-1, 1), ylim=c(0, 2), 
     xaxt='n', yaxt='n', xlab=NA, ylab=NA, bty='n')

ArtPoon

require(ape)

#' get.intervals
#' 
#' Scan through BEAST tree log line-by-line and parse each 
#' Newick string to retrieve the coalescent intervals
#' 
#' @param treefile: (character) relative or absolute path to trees log file
#' @return List containing objects of class coalescentIntervals (ape) keyed
#'         by state (MCMC step number)

ArtPoon

import os
import sys
import csv
from glob import glob
import argparse

from micall.core.parse_interop import read_errors, write_phix_csv
from micall.core.filter_quality import report_bad_cycles
from micall.core.censor_fastq import censor
from micall.core.prelim_map import prelim_map

ArtPoon

require(ggfree)

# prep lists of data
attach(pheno.sel)
l1 <- split(Oil[Exp=='IHO'], Year[Exp=='IHO'])
l2 <- split(Oil[Exp=='ILO'], Year[Exp=='ILO'])

# ILO missing data for 1985
z <- which(names(l2)=='1984')
l2 <- c(l2[1:z], list('1985'=numeric(0)), l2[(z+1):length(l2)])

ArtPoon

add.grid <- function(fg.col='white', bg.col='ivory2', lwd.major=3, lwd.minor=1) {
  # call this after plot() but *before* drawing any data with points() or lines()
  u <- par('usr')  # get plot region dimensions
  x <- par('xaxp')
  y <- par('yaxp')
  
  # fill background
  rect(xl=u[1], yb=u[3], xr=u[2], yt=u[4], col=bg.col, border=NA)
  
  x.major <- seq(x[1], x[2], length.out=x[3]+1)

ArtPoon

import urllib.request as ur, random, json, webbrowser
aid=','.join([str(random.randint(0,4e6)) for i in range(20)])
r=ur.urlopen("https://itunes.apple.com/lookup?amgAlbumId="+aid)
res=json.loads(r.read())
album=res['results'][0]['collectionViewUrl']
webbrowser.open(album)

ArtPoon

get.terminals <- function(node, tree) {
	parents <- c(node)
	tips <- c()
	while (length(parents) > 0) {
		for (parent in parents) {
			children <- tree$edge[which(tree$edge[,1]==parent),2]
			parents <- parents[parents!=parent]
			if (length(children) > 0) {
				parents <- c(parents, children)
			} else {

ArtPoon

import argparse
from suds.client import Client
import sys
import re

def iter_fasta (handle):
    header = None
    sequence = ''
    for line in handle:
        if line.startswith('$'):