Metadata-Version: 2.1
Name: transcriptorthology
Version: 3.0.1
Summary: Algorithm to address Orthology and Paralogy at the Transcript Level
Home-page: https://github.com/UdeS-CoBIUS/TranscriptOrthology
Author: Wend Yam Donald Davy Ouedraogo
Author-email: wend.yam.donald.davy.ouedraogo@usherbrooke.ca
License: MIT
Keywords: clustering,alternative splicing,orthology-paralogy inference,isoorthology,algorithm,evolution,transcripts,phylogeny,computational-biology
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Description-Content-Type: text/markdown


# Inferring clusters of orthologous and paralogous transcripts

``Algorithm to infer clusters of isoorthologous transcripts using gene-level homology relationships and a Reciprocal Best Hits approach``

![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/rainbow.png)

<!-- ABOUT THE PROJECT -->
<h2 id="about-the-project">About The Project</h2>


<!-- OVERVIEW -->
<h3 id="overview">Overview</h3>

`A graph-based method to infer isoorthology & recent paralogy relations in a set of homologous transcripts`

---


<!-- Requirements -->
<h3 id="requirements"> Requirements</h3>

*   __`python3 (at leat python 3.6)`__
*   __`NetworkX`__
*   __`Pandas`__
*   __`Numpy`__
*   __`ETE toolkit`__


![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/rainbow.png)

<!-- Package -->
<h3 id="package">About the package</h3>

``install the package``
<pre><code>pip3 install transcriptorthology</code></pre>

``import package and use the main function``
<pre><code>from transcriptorthology.transcriptOrthology import inferring_transcripts_isoorthology


if __name__ == '__main__':
  gtot_path = './execution/mapping_gene_to_transcripts/ENSGT00390000003967.fasta'
  gt_path = './execution/NHX_trees/ENSGT00390000003967.nhx'
  lower_bound = 0.7
  transcripts_msa_path = './execution/transcripts_alignments/ENSGT00390000003967.alg'
  tsm_value = 1
  output_folder = './execution/output_folder'
  
  <span style="color:red;">inferring_transcripts_isoorthology</span>(<span style="color:red;">transcripts_msa_path</span>, <span style="color:green;">gtot_path</span>, <span style="color:purple;">gt_path</span>,<span style="color:orange;">tsm_value</span>,<span style="color:yellow;">lower_bound</span>,<span style="color:gray;">output_folder</span>)</code></pre>


![-----------------------------------------------------](https://raw.githubusercontent.com/andreasbm/readme/master/assets/lines/rainbow.png)

---
<br>
<br>
<br>
<br>
<br>
<br>
Copyright © 2023 CoBIUS LAB






