adamewing

#

adamewing

#!/usr/bin/env python

import sys
import os
import argparse
import subprocess
import pysam
import tempfile
import multiprocessing as mp
import re

adamewing

#!/usr/bin/env python

import sys
import pandas as pd

import matplotlib as mpl
# Force matplotlib to not use any Xwindows backend.
mpl.use('Agg')
import matplotlib.pyplot as plt

adamewing

#!/usr/bin/env python

import sys

import pandas as pd
import numpy as np


from collections import defaultdict as dd

adamewing

dataList <- readRDS("ExpressionList_QC_norm_clustered_clean.rds")

m <- dataList[[1]]
pD <- dataList[[2]]
fD <- dataList[[3]]

library(dplyr)
library(edgeR)

comps <- list(C12v14=c("C12","C14"), C13v14=c("C13","C14"))

adamewing

#!/usr/bin/env julia

import Printf: @printf
import Base: parse


function contig_dict(vcf_fn)
    ctgs = Dict{String,Int64}()

    open(vcf_fn) do vcf

adamewing

#!/usr/bin/env python

from __future__ import print_function

import sys

'''
Parses records that look like:

  276  28.4  0.0  1.2  chr1       837099  837180 (248119242) +  SVA_D          Retroposon/SVA         131  211 (1175)   1082

adamewing

#!/usr/bin/Rscript

library(statmod)
library(ggplot2)
library(reshape2)

num_samples <- 10

pow <- matrix(nrow=(num_samples+1), ncol=(num_samples+1))

adamewing

#!/usr/bin/env python

from collections import defaultdict as dd
from bx.intervals.intersection import Intersecter, Interval

def interval_forest(bed_file):
    ''' build dictionary of interval trees '''
    forest = dd(Intersecter)

    with open(bed_file, 'r') as bed:

adamewing

#!/usr/bin/env python

'''
Simple copy number profiling script for tumour / normal pairs.

Adam Ewing
adam.ewing@mater.uq.edu.au

'''