README.md

HTSinfer

HTSinfer infers metadata from High Throughput Sequencing (HTS) data.

Usage

htsinfer [-h] -f1 FILE [-f2 FILE] [-n INT] [-o STR] [--verbose] [--debug] [--version]

Parameters

required arguments:
  -f1 FILE, --file-1 FILE
      file path to read/first mate library

optional arguments:
  -f2 FILE, --file-2 FILE
      file path to second mate library
  -n INT, --max-records INT
      maximum number of records to process, starting with
      first record; set to 0 to process entire file(s)
  --verbose, -v
      print logging messages to STDERR
  --debug
      print debugging messages to STDERR
  --version
      show version information and exit
  -h, --help
      show this help message and exit

Installation

In order to use the HTSinfer, clone the repository and install the dependencies with Conda:

git clone https://github.com/zavolanlab/htsinfer
cd htsinfer
conda env create --file environment.yml
conda env update --file environment-dev.yml  # optional: install development/testing dependencies
conda activate htsinfer
python setup.py install

If you have installed the development/testing dependencies, you can verify that HTSinfer was installed correctly by executing the tests shipped with the package:

python -m pytest

Run HTSinfer via the CLI script htsinfer as described in the Usage section.

Contributing

This project lives off your contributions, be it in the form of bug reports, feature requests, discussions, or fixes and other code changes. Please refer to the contributing guidelines if you are interested to contribute. Please mind the code of conduct for all interactions with the community.

Contact

For questions or suggestions regarding the code, please use the issue tracker. For any other inquiries, please contact us by email: [email protected]

(c) 2020 Zavolan lab, Biozentrum, University of Basel