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# |
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#!/usr/bin/env python | |
import sys | |
import os | |
import argparse | |
import subprocess | |
import pysam | |
import tempfile | |
import multiprocessing as mp | |
import re |
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#!/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 |
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#!/usr/bin/env python | |
import sys | |
import pandas as pd | |
import numpy as np | |
from collections import defaultdict as dd |
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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")) |
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#!/usr/bin/env julia | |
import Printf: @printf | |
import Base: parse | |
function contig_dict(vcf_fn) | |
ctgs = Dict{String,Int64}() | |
open(vcf_fn) do vcf |
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#!/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 |
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#!/usr/bin/Rscript | |
library(statmod) | |
library(ggplot2) | |
library(reshape2) | |
num_samples <- 10 | |
pow <- matrix(nrow=(num_samples+1), ncol=(num_samples+1)) |
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#!/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: |
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#!/usr/bin/env python | |
''' | |
Simple copy number profiling script for tumour / normal pairs. | |
Adam Ewing | |
adam.ewing@mater.uq.edu.au | |
''' |
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