Metadata-Version: 2.1
Name: pysalsa
Version: 0.1.0
Summary: convert between bioinformatics formats
Author: The biomics Contributors
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: Thomas Cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: BSD
Keywords: NGS
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Provides-Extra: testing
License-File: LICENSE

SALSA
======

Set of scripts related to biomics projects and provided by the SALSA group 



.. image:: https://badge.fury.io/py/salsa.svg
    :target: https://pypi.python.org/pypi/salsa

.. image:: https://github.com/biomics-pasteur-fr/salsa/actions/workflows/main.yml/badge.svg?branch=main
    :target: https://github.com/biomics-pasteur-fr/salsa/actions/workflows/main.yml

.. image:: https://coveralls.io/repos/github/biomics-pasteur-fr/salsa/badge.svg?branch=main
    :target: https://coveralls.io/github/biomics-pasteur-fr/salsa?branch=main




:Python version: 3.7, 3.8, 3.9
:Issues: `On github <https://github.com/biomics-pasteur-fr/salsa/issues>`_

Tutorial
=========

comute-test sub command
-----------------------

Compute ttest of a input file that contains two groups of genes with their log2 fold change and pvalues. Input file has this header::

    gene, Group1_sample1_L2FC, Group1_sample2_L2FC, Group1_sample3_L2FC, Group1_sample4_L2FC, 
          Group1_sample5_padj, Group1_sample6_padj, Group1_sample7_padj, Group1_sample8_padj, 

where Group1 and Group2 are tag to defined the two groups, and log2FoldChange and padj two patterns to set the log Fold change and adjuster pvalues columns. This names can be set to whatever string since options can be used to specify them. 

See an example in test/data/test_compute_ttest.csv

:: 

   salsa compute-ttest --infile test.csv --outpfile out.csv --name-group1  Group1 --name-group2 Group2  \
       --name-log2-foldchange L2FC --name-log2-foldchange L2FC




