nextHIV

Description

Processing code for nextHIV. The package skeleton was created using makenew/python-package.

Docker installation

Local installation

Source Code

The nexthiv source is hosted on GitHub. Clone the project with

git clone https://github.com/sdwfrost/nexthiv.git

Requirements

You will need Python 3 with pip.

Install the dependencies with

pip install -r requirements.txt

Usage

Configuration

Configuration for the database is stored as a YAML document, An example is found below.

rethinkdb:
  host: 'localhost'
  port: 28015
  db: 'nexthiv'
tables:
  - sequences
  - processed_sequences
  - demographics
  - regimens
  - labs
  - references
  - resistance
  - subtypes
  - clustering
  - phylogenies
sequence:
  table: 'sequences'
  name: 'SEQUENCE'
  startpos: 0
  endpos: 1497
  processed_table: 'processed_sequences'
  processed_name: 'SEQUENCE_ALIGNED'
directories:
  datadir: './data'
  tmpdir: './tmp'
programs:
  mafft:
    cmd: 'mafft'
  tn93:
    cmd: 'tn93'
    threshold: 1.0
    ref_threshold: 0.05
    ambiguities: 'resolve'
    min_overlap: 100
    fraction: 1.0
  iqtree:
    cmd: 'iqtree-omp'
    threads: 4
    model: 'GTR+G4'
    bootstrap_samples: 1000

Initialising database

nexthiv init -c nexthiv.yaml

Importing data

nexthiv import -c nexthiv.yaml -i sequences.txt -d sequences

Aligning sequences

The following command will align the sequences against a reference, trim them, and insert them into the processed_sequences table.

nexthiv align -c nexthiv.yaml

Clustering sequences

nexthiv cluster -c nexthiv.yaml

Contributing

Please submit and comment on bug reports and feature requests.

To submit a patch:

1. Fork it (https://github.com/sdwfrost/nexthiv/fork).
2. Create your feature branch (git checkout -b my-new-feature).
3. Make changes. Write and run tests.
4. Commit your changes (git commit -am 'Add some feature').
5. Push to the branch (git push origin my-new-feature).
6. Create a new Pull Request.

License

This Python package and associated files are licensed under the MIT license.

Warranty

This software is provided "as is" and without any express or implied warranties, including, without limitation, the implied warranties of merchantibility and fitness for a particular purpose.