An automated Python proviral intactness checker for HIV-1 consensus sequences.
The pipeline is written in Python 3. The below installation instructions assume that Python 3 is already present on the system. If not, it can be installed via a package manager, e.g. for Debian-based systems:
sudo apt install python3
or for RedHat-based systems:
sudo yum install python3
or for Macintosh-based systems:
sudo port install python3
Installation on Windows systems is not recommended.
In addition, for local installations, pip and virtualenv are also required, and can be installed using the commands listed above.
Finally, the pipeline requires that the MAFFT multiple sequence aligner be installed. Again, one of:
sudo apt install mafft
sudo yum install mafft
sudo port install mafft
depending on your operating system, should get you there.
Install with:
git clone --recurse-submodules [email protected]:ramics/intactness-pipeline
cd intactness-pipeline
virtualenv -p python3 env
env/bin/pip install .
Install with:
git clone --recurse-submodules [email protected]/ramics/intactness-pipeline
cd intactness-pipeline
python3 setup.py build
sudo python3 setup.py install
Whichever way you choose to install, you'll get a number of warnings if tools needed by the pipeline or one of its dependencies aren't in your path, along with links to download and install those dependencies.
If you've installed locally, you need to activate the Python environment by running source env/bin/activate.
Then run on a set of FASTA sequences with:
proviral intact --subtype B sequences.fasta
See help (including how to switch various intactness tests on and off) at:
proviral intact --help
Currently available subtypes can be seen by listing the util/subtype_alignments folder.
This will return four files:
intact.fasta: all consensus sequences considered to be intact.nonintact.fasta: all consensus sequences not considered to be intact.orfs.json: locations of ORFs in all sequences.errors.json: a JSON dump of the reasons why some sequences were considered not intact.
We're using git flow for this project. The package git-flow can be installed on most OSes. To get started, go to the provirus-pipeline repo on your machine and type:
git flow init
Press enter until you hit the command line again. Then, to develop a feature, say the ability to detect long deletions, type:
git flow feature start long-deletions
You'll now be on a feature branch. If you'd like other people to collborate on your feature branch, you'll need to publish it. Type:
git flow feature publish long-deletions
Hack away until you're satisfied, then type:
git flow feature finish long-deletions
Follow the instructions, and this will merge your feature into develop. You can then git push to develop, and your feature will be included in the next release.
A release is a merge to master. The master branch of this github repo is blocked with a review guard, meaning before you merge develop into master, you need to open a pull request on github from develop into master and get it reviewed by another contributor. This is to keep code quality high.
Please bump at least the minor version in setup.py with every release.
To reinstall locally without reinstalling dependencies or bumping the version, run:
env/bin/pip install --force-reinstall --no-deps --upgrade .