slowkow

#!/usr/bin/env bash
# bigWigRegions
# Kamil Slowikowski
#
# Depends on bigWigToBedGraph: http://hgdownload.cse.ucsc.edu/admin/exe/

if [[ $# -ne 2 ]]; then
    echo "bigWigRegions - Print bigWig data for each region in a bed file."
    echo -e "usage:\n   bigWigRegions in.bigWig in.bed > out.bedGraph"
    echo "   bigWigRegions in.bigWig <(zcat in.bed.gz) > out.bedGraph"

slowkow

function cd_dir_history()
{
    OLDPWD="$PWD"
    echo "# $(date) $USER -> $@" >> "$HISTFILE"

    command cd "$@"

    # If this directory is writable then write to directory-based history file
    # otherwise write history in the usual home-based history file.
    touch "$PWD/.dir_bash_history" 2>/dev/null \

slowkow

#!/usr/bin/perl
# Author      : Kamil Slowikowski <kslowikowski@gmail.com>
# Date        : March 23, 2011
# Version     : 0.1
# Description : Modified code from
#               http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook

use strict;
use warnings;

slowkow

# https://www.biostars.org/p/162853

cache = {}

f2 = open('f2')
header2 = f2.next()

for line in f2:
    fields = line.strip().split()
    snp = fields[0]

slowkow

#!/usr/bin/env python

"""merge_intervals.py

Merge tab-delimited intervals:

    cat tissue1.txt 
    chr1,1-2
    chr1,3-4
    chr1,5-6

slowkow

#!/usr/bin/env python

"""ncbi_fetch.py

Query NCBI and fetch the results into gzipped files. Files will be saved in
the current directory as: 001-050.gz, 051-100.gz, etc.

You can then do:

    zcat 001-050.gz | head

slowkow

"""
genomic_intervals.py
Kamil Slowikowski
February 27, 2014

Genomic intervals: 0-based, 1-based, overlaps, and distance
===========================================================

This document describes genomic intervals and includes source code for testing
overlap and calculating distance between intervals.

slowkow

"""
chromtree.py
Kamil Slowikowski
October 30, 2013

This module is a simple extension of

    bx.intervals.intersection.IntervalTree

to neatly handle a dictionary of interval trees.

slowkow

#!/usr/bin/env python
# encoding: utf8
"""
merge_lanes.py
Kamil Slowikowski
July 17, 2015

Broad Technology labs provides sequencing data in a directory structure like
this:

slowkow

#!/usr/bin/env python
"""
Kamil Slowikowski

fix_alleles.py
==============

Change the alleles in a dosage file to match the alleles specified in
a separate reference file. If a variant is not present in the reference file,
then it will not be changed.