Obi

Conda Install

Conda package can be found in https://anaconda.org/jcalvento/obi. To install, run:

• conda install -c jcalvento obi --channel bioconda

Usage

For each script you can get arguments description and usage by using --help argument. i.e. obi --help

There are the available commands, each one has its own parameters. Use obi <command> --help to learn more about the usage

obi fetch-db                  Downloads Swissprot DB and Uniprot <-> PDB mappings from NCBI FTP server
obi run [<args>]              Runs the whole analysis or first part depending on the arguments
obi analysis [<args>]         Runs positive selection analysis, which includes running Hyphy and getting final results
obi resume-analysis [<args>]  Runs the whole analysis or first part depending on the arguments

Setup

• Install Conda or Miniconda (if you want a lightweight version)

• Create conda env with Python 3.7.* using requirements from environment.yml file. i.e. conda env create --file environment.yml python=3.7

• Download Swissprot DB and Uniprot <-> PDB mappings from NCBI FTP server. You simply run obi\ fetch-db if you installed it as a Conda package, or use the fetch_db.py script (python src/scripts/fetch_db) when you are in the development env

Analysis entrypoint

To run the whole analysis or first part depending on the arguments, you can use obi\ run --help

usage: obi run [-h] [--fasta FASTA] [--email EMAIL] [--output-path OUTPUT_PATH] [--blast BLAST] [--min-identity MIN_IDENTITY] [--max-evalue MAX_EVALUE] [--min-coverage MIN_COVERAGE]
               [--max-gaps MAX_GAPS] [--include-analysis] [--mode MODE]

optional arguments:
  -h, --help            show this help message and exit
  --fasta FASTA         Path of the Fasta file containing the problem sequence
  --email EMAIL         Email to register while using Entrez
  --output-path OUTPUT_PATH
                        Directory where the program creates output files. Default: ./results/<fasta-filename>
  --blast BLAST         Path to Blast Swissprot DB. Default: ./swissprot/swissprot
  --min-identity MIN_IDENTITY
                        Minimum identity percentage for Blast query expressed as float. Default: 0.4
  --max-evalue MAX_EVALUE
                        Max evalue permitted for Blast results. Default: 0.005
  --min-coverage MIN_COVERAGE
                        Min coverage permitted for Blast results. Default: 90
  --max-gaps MAX_GAPS   Maximum number of gaps permitted for Blast results. Default: 6
  --include-analysis    If present, runs positive selection analysis, which includes running Hyphy and getting final results. If not present, result includes until nucleotide alignment
  --mode MODE           Only used when --include-analysis is present. "local" if you want to run Hyphy locally, "remote" to use Datamonkey instead. Default: local

For development env use python obi/scripts/run.py

Only analysis

To run only the analysis (if previous step didn't include it) use obi\ analysis

usage: obi analysis [-h] [--input-path INPUT_PATH] [--mode MODE] [--email EMAIL]

optional arguments:
  -h, --help            show this help message and exit
  --input-path INPUT_PATH
                        Path of alignment preparation result
  --mode MODE           "local" if you want to run Hyphy locally, "remote" to use Datamonkey instead. Default: local
  --email EMAIL         Required when running in remote mode. You will get notified once job is done

For development env use python obi/scripts/analysis.py

Resume remote analysis

Run obi\ resume-analysis

usage: resume [-h] [--input-path INPUT_PATH]

optional arguments:
  -h, --help            show this help message and exit
  --input-path INPUT_PATH
                        Path of alignment preparation result

For development env use python obi/scripts/resume_analysis.py

Running an example

An input file example can be found in the examples directory. The input fasta file, containing the Human Hemoglobing, can be analyzed by running:

obi\ run --fasta /home/ana/user/examples/P68871_HBB/hb_homo_sapiens.fasta --mode local --email [email protected]

Check the setup section before running your analysis

Conda Build

• Run conda build conda.recipe -c bioconda -c anaconda -c conda-forge -c defaults
• Convert build to different for distributions (OSx, Linux & Windows, remove current one): conda convert path/to/obi/build/obi-x.x.x-x.tar.bz2 -p linux-64 -p win-64 -p osx-64 -p ...
• Upload: anaconda upload /path/to/build.tar.bz2

Collaborate with Obi project

The OBI project is open to contributions. Create a branch with your changes and open a pull request, so we can review it. All checks should pass before merging into main branch.

Questions and issues

Open an issue with question and/or problems