davmlaw

#!/bin/bash

set -e # Fail on error

# We can wipe this once we move this to public servers
if [ -z ${GITHUB_USER} ]; then
    echo "Please set the variable GITHUB_USER used to download variantgrid and bioinformatics projects"
    exit 1; 
fi
if [ -z ${GITHUB_PASSWORD} ]; then

davmlaw

#!/usr/bin/env python

import matplotlib.pyplot as plt
import numpy as np

LATEX_BASELINE = 0.1
FUNDIES = 20
BIRTH_CONTROL_INVENTION=0.1
FUNDIE_ARROW_OFFSET = 0.1

davmlaw

#!/usr/bin/env python

import os
import sys

if len(sys.argv) != 2:
    print "Usage %s: samtools_index" % os.path.basename(sys.argv[0])
    sys.exit(1)

samtools_index = sys.argv[1]

davmlaw

def sam_or_bam_has_chrom(sam_or_bam_filename):
    ''' return true if sam or bam has chr in header reference names
        warning: this will die if you have BOTH chr and NO chr
    '''
    sf = pysam.Samfile(sam_or_bam_filename, "rb")
    header_dict = sf.header
    
    sq = header_dict['SQ']
    has_chr = 0
    no_chr = 0

davmlaw

import itertools

print [''.join(s) for s in itertools.permutations("ACGT")]