Metadata-Version: 2.2
Name: genemapper
Version: 1.0.1
Summary: A command-line tool for retrieving GenBank metadata and mapping coding sequences between query and subject FASTA files to identify their most similar counterparts.
Author-email: Mohammed Salim Dason <mohammed.dason@polito.it>
Maintainer-email: Mohammed Salim Dason <mohammed.dason@polito.it>
License: MIT license
Project-URL: bugs, https://github.com/salimdason/genemapper/issues
Project-URL: changelog, https://github.com/salimdason/genemapper/blob/master/changelog.md
Project-URL: homepage, https://github.com/salimdason/genemapper
Description-Content-Type: text/x-rst
License-File: LICENSE
License-File: AUTHORS.rst
Provides-Extra: dev
Requires-Dist: coverage; extra == "dev"
Requires-Dist: mypy; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Requires-Dist: ruff; extra == "dev"

GeneMapper
==========

|PyPI version| |Build Status| |Documentation Status| |BioPython| |Pandas| |Python version|

A command-line tool for retrieving GenBank metadata and mapping coding
sequences between query and subject FASTA files to identify their most
similar counterparts.

-  **Free software**: MIT license
-  **Documentation**: https://genemapper.readthedocs.io

Features
--------

-  Automated retrieval of GenBank metadata for query and reference
   sequences files in FASTA format.
-  Parallelized mapping of query CDS against subject CDS with scoring
   and threshold-based similarity.
-  Detailed log and Excel output of mapping results
-  Adjustable similarity thresholds and multi-processor usage.

Installation
------------

.. code:: bash

   pip install genemapper

Usage - Metadata Retrieval
--------------------------

.. code:: bash

    genemapper metadata --query my_query_gene_cds.fasta --reference my_subject_gene_cds.fasta --email you@example.com

Usage - Gene Mapping
--------------------

.. code:: bash

    genemapper map --query my_query_gene_cds.fasta --subject my_subject_gene_cds.fasta --output LAbriniVersusCAETHG_Mapping.xlsx --similarityThreshold 0.99 --numProcesses 20

.. |PyPI version| image:: https://img.shields.io/pypi/v/genemapper.svg
   :target: https://pypi.python.org/pypi/genemapper
   :alt: PyPI version

.. |Build Status| image:: https://img.shields.io/travis/salimdason/genemapper.svg
   :target: https://travis-ci.com/salimdason/genemapper
   :alt: Build Status

.. |Documentation Status| image:: https://readthedocs.org/projects/genemapper/badge/?version=latest
   :target: https://genemapper.readthedocs.io/en/latest/?version=latest
   :alt: Documentation Status

.. |BioPython| image:: https://img.shields.io/badge/BioPython-1.78-brightgreen
   :target: https://biopython.org
   :alt: BioPython

.. |Pandas| image:: https://img.shields.io/badge/Pandas-%3E%3D1.0.0-blue
   :target: https://pandas.pydata.org
   :alt: Pandas

.. |Python version| image:: https://img.shields.io/pypi/pyversions/genemapper.svg
   :target: https://www.python.org/
   :alt: Python version
