brentp

usage:

shuf.sh "bedtools cmd" "metric" $genome

where metric must accept the output from bedtools cmd and return a single numeric value.

brentp

# -*- coding: utf-8 -*-

u"""
Beta regression for modeling rates and proportions.

References
----------
Grün, Bettina, Ioannis Kosmidis, and Achim Zeileis. Extended beta regression
in R: Shaken, stirred, mixed, and partitioned. No. 2011-22. Working Papers in
Economics and Statistics, 2011.

brentp

"""
Compare speed of a cython wrapper vs a cffi wrapper to the same underlying
C-code with a fast function and a longer-running function.

This should run anywhere that has cffi and cython installed.

Ouput on my machine with python2.7:


brentp@liefless:/tmp$ python compare-wrappers.py

brentp

library(SKAT)
set.seed(1)

hap.skat.null = function(formula, covs, ...){
    covs = read.delim(covs)
    assign("y", covs[[as.character(formula[[2]])]], envir = .GlobalEnv)
    m = SKAT_Null_Model(formula, data=covs, out_type="D")
    return(m)
}

brentp

add a readgroup to a bam doesn't need the entire "@RG\t..." just a single id.

addrg some.bam my-id > some.rg.bam

or

generate-bam | addrg - > some.rg.bam

brentp

/*
 * example for me to learn khash.h library from lh3
 */

#include "khash.h"
#include <stdio.h>

// int keys and char * values
KHASH_MAP_INIT_INT(ihash, char *)

brentp

library(SNPRelate)
library(FDb.UCSC.snp137common.hg19)
library(hash)

args = commandArgs(TRUE)

vcf.fn = args[1]


gds.fn = paste0(args[1], ".gds")

brentp

"""
align reads with bwa mem 
remove duplicates with samblaster
call variants with freebayes
"""
import sys
import os.path as op
import os

def base(fq):

brentp

"""
use cruzdb to annotate the illumina 450K manifest file with
position relative to gene and to CpG
"""
import sys
import os.path as op
from cruzdb import Genome
from toolshed import reader

if not op.exists('hg19.db'):

brentp

"""
create a BED file with position and strand given the genes from a
TCGA level 3 expression matrix
"""
from cruzdb import Genome
from toolshed import reader
import sys
import os.path as op

matrix = sys.argv[1] # has a column named "probe" that is a refGen name