pmagwene

nr1 = np.core.records.fromarrays(d1.transpose(), names=labels,formats=['f8']*191)

pmagwene

from yeastgenome import samsnp
from yeastgenome import yeastgff as yff
from yeastgenome import yeastsnp
from yeastgenome import gff, gffsnp as gs


flist = gff.parse_GFFfeatures('./yeast-genome-Feb2011/saccharomyces_cerevisiae.gff')
gdict = gff.fasta_asdict('../yeast-genome-feb2011/saccharomyces_cerevisiae.gff')

bwa70 = samsnp.parse_samsnp('./PMY070/bwa.Feb2011/final.pileup')

pmagwene

If you want to change this behavior, open Terminal.app and type

defaults write com.macromates.textmate OakDisableSessionRestore 1

This will make Textmate not remember the last session.

Change the 1 by 0 if you want the default behavior.

pmagwene

# assumes pyplot and numpy are in namespace

import string
x = [1,4,5,9,9,11,13,14,18,20]
cats = [i for i in string.letters[:10]]
maxx = max(x)*1.10
ax = axes([0,0,1,1])
xlim(0,maxx)
ylim(0,11)
ticks = ax.yaxis.set_ticks(range(1,11))

pmagwene

If using brew version of python

Make sure you brew as:

brew install --framework python

Configure

pmagwene

\documentclass[10pt]{article}
\usepackage[usenames]{color} %used for font color
\usepackage{amssymb} %maths
\usepackage{amsmath} %maths\documentclass[10pt,letterpaper]{article}

%\usepackage[usenames]{color} %used for font color
\usepackage[HTML,dvipsnames,svgnames,x11names,hyperref]{xcolor}
\usepackage{amssymb} %maths
\usepackage{amsmath} %maths
\usepackage[utf8]{inputenc} %useful to type directly diacritic characters

pmagwene

samtools mpileup -uf ../../yeast-genome-Feb2011/yeast-genome-Feb2011.fasta aln.sorted.bam | bcftools view -bvcg - > var.raw.bcf


bcftools view var.raw.bcf | vcfutils.pl varFilter -D400 > var.flt.vcf 

pmagwene

# https://github.com/matplotlib/matplotlib/issues/881
# Several of the ColorBrewer maps are "qualitative", meaning
# they are just a group of colors that can be used together 
# for categories of data.  So I remapped Accent to segments 
# instead of continuous:

# Actually, these should be used with ListedColormap, and 
# the number of colors should depend on the number of 
# categories in the data, with colors removed from the 
# list in a certain order?

pmagwene

{
 "metadata": {
  "name": "",
  "signature": "sha256:4632c48d2d93ec86103808ed599b94a33dfdda25ab937192359f68ab92ee1ec0"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [

pmagwene

library(tidyr)
library(dplyr)
library(magrittr)
library(ggplot2)

# load data in "wide" format (genes in columns)
spellman <- read.csv("spellman-reformated.csv")

# restructure in "long" format
spellman.long <- gather(spellman, gene, expression, -expt, -time)