Metadata-Version: 2.4
Name: tnatlas
Version: 0.0.3
Summary: Find transposon integrations in reads and align them to genomes.
Author-email: Lewis Grozinger <lewis.grozinger@cnb.csic.es>, Ana Mariya Anhel <a.valdes@liverpool.ac.uk>, Lorea Alejaldre <lorea.alejaldre@cnb.csic.es>, Angel Goni Moreno <angel.goni@cnb.csic.es>
Maintainer-email: Lewis Grozinger <lewis.grozinger@cnb.csic.es>
License-Expression: MIT
Keywords: bioinformatics,alignment,genetics,transposon,scientific
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE.txt
Requires-Dist: biopython>1.8
Requires-Dist: numpy>2.2
Requires-Dist: pandas
Requires-Dist: openpyxl
Requires-Dist: psutil
Dynamic: license-file

# Overview

TnAtlas is a Python package for identifying and annotating transposon integration events into genomes.

Given a set of sequencing reads, transposon sequences, and genomes, the TnAtlas package can:

* Looks for reads which contain genomic DNA preceded by transposon DNA.
* Annotating the reads with corresponding features from the genome.
* Produces a summary for a set of reads in excel format.

For those who *do not want to write Python code*, the package also ships with 2 utilities, `tnfind` and `tnmeta`, which can be used to run analysis from the command line. 

# Installing

## Dependencies

* Python >= 3.8 
* blastn >= 2.12

### Optionally
Some parts of the pipeline also require

* fastqc (for sequencing quality control reports)
* sickle (for trimming based on sequencing quality)

## From source code

1. Get the code:
   
   `git clone https://github.com/lgrozinger/transposonaligner`
3. Install using pip:
   
   `python3 -m pip install ./transposonaligner`

## From PyPI (using pip)

Coming soon to PyPI...

# Usage

# Contributing

Contributions of all kinds are welcomed, including:
* Code for new features and bug fixes
* Test code and examples
* Bug reports and suggestions for new features (e.g. opening a github issue)

If you plan to change the source code, please open an issue for discussing the proposed changes and fork the repository.

# Citing

If you use this work as part of a publication, please cite as: ___________________

# Acknowledgements
