Description

This repository contains scripts, wrappers or snippets of code useful for converting format ( bigBed, bigWig, etc. ) and creating track hubs.

Getting Started

First copy the application binaries

cd scripts 
./copy_ucsc_exe

and grab chrom.sizes from UCSC using the chosen assembly e.g.

mkdir ../local
./fetchChromSizes hg38 > ../local/hg38.chrom.sizes

Perform any operation necessary to prepare the files that will be used to create tracks, such as

# set uniform color in BED files...
./set_bed_color BED1.bed BED2.bed.gz 265,165,0
# ... remove selected contigs, adjust score, etc.
header=$(zcat BED1.bed.gz | sed -n '1p') && zcat BED1.bed.gz | tail $1 -n+2 | awk 'BEGIN{FS=OFS="\t";}{print $1,$2,$3,$4,100,$6,$7,$8,$9,$10,$11,$12;}' | awk '$1!~"AEMK|FPK"' | sed "1s/^/$header\n/g" | gzip > BED2.bed.gz
# reheader BAM files to match UCSC contig format...
./reheader_bam DIR1 DIR2 hg38
# ... or run any other custom script to convert GTF, BED6 to BED12, or bedGraph.

Prepare the indexed binary files (bigBed, bigWig) by running one of the following get_bed2bigBed.py, get_bam2bigWig.py, or get_bedGraph2bigWig.py. These scripts are wrapper to Genome Browser application binaries or deepTools executables such as bamCoverage. For more information, use the --help\-h option.

Prerequisites

Pinned version of selected dependencies are listed in the requirements.txt file for reproducible installation, in particular the Python package trackhub and deepTools.

Note: it may be a good idea to re-install the trackhub package from latest pip install git+git://github.com/daler/trackhub@master.

A number of UCSC Genome Browser application binaries for stand-alone use are also required and can be copied using the script copy_ucsc_exe.

Installation

To install the local VCS project in development mode, use the --editable or -e option, otherwise this flag can be ignored.

To install phub and dependencies, first create a virtual environment:

python3 -m venv /path/to/virtual/environment

For information about Python virtual environments, see the venv documentation. To activate the new virtual environment and install phub:

# Activate the new virtual environment.
source /path/to/virtual/environment/bin/activate

# If necessary, upgrade pip and wheel or additional packages (such as setuptools if installing in editable mode).
pip install --upgrade pip setuptools wheel

# Clone the git repository
git clone https://github.com/eboileau/trackhub-utils
cd trackhub-utils

# The period is required, it is the local project path (trackhub-utils)
pip --verbose install -r requirements.txt [-e] . 2>&1 | tee install.log

Anaconda installation

The package can also be installed within an anaconda environment.

# Create the anaconda environment.
conda create -n my_new_environment python=3.6 anaconda

# Activate the new environment.
source activate my_new_environment

# Clone the git repository
git clone https://github.com/eboileau/trackhub-utils
cd trackhub-utils

pip --verbose install -r requirements.txt [-e] . 2>&1 | tee install.log

Uninstallation

To remove the phub package:

pip uninstall phub

If the package is installed in a dedicated virtual environment, this environment can also be cleared or removed.

Running the tests

Contributing

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

Some scripts/utils are adapted from the pybio-utils package, authored by Brandon Malone, and maintained by Etienne Boileau.