Metadata-Version: 2.1
Name: frags
Version: 0.1.5
Summary: Finding recombinations in reads
Home-page: https://gitlab.pasteur.fr/nmaillet/frags
Author: Maillet Nicolas
Author-email: nicolas.maillet@pasteur.fr
License: UNKNOWN
Project-URL: Doc, https://frags.readthedocs.io/en/latest/
Description: Find Recombinations Among Genomes (FRAGS)
        =========================================
        
        Find Recombinations Among Genomes (FRAGS) is a software dedicated to analyze recombinations in viral genomes.
        
        .. image:: https://badge.fury.io/py/frags.svg
            :target: https://badge.fury.io/py/frags
            :alt: Pypi repo
        
        .. image:: https://gitlab.pasteur.fr/nmaillet/frags/badges/master/pipeline.svg
            :target: https://gitlab.pasteur.fr/nmaillet/frags/commits/master
            :alt: Build Status
        
        .. image:: https://gitlab.pasteur.fr/nmaillet/frags/badges/master/coverage.svg
            :target: https://gitlab.pasteur.fr/nmaillet/frags/commits/master
            :alt: Coverage Report
        
        .. image:: https://readthedocs.org/projects/frags/badge/?version=latest
            :target: https://frags.readthedocs.io/en/latest/?badge=latest
            :alt: Documentation Status
        
        :note: FRAGS is tested with Gitlab Ci for the following Python version: 3.7 to 3.8
        :issues: Please use https://gitlab.pasteur.fr/nmaillet/frags
        
        
        
        Overview
        ========
        
        Find Recombinations Among Genomes (FRAGS), is a standalone software dedicated to identify reads coming from recombination events.
        
        FRAGS is a python tool taking fasta/fastq files of reads as input and one or two reference genomes. It then identifies chimeric reads (reads composed of non-adjacent fragsments, coming either from on one or the two references genomes) and potential breakpoints (insert between fragsments). Optionally, breakpoints can then be Blasted again the host genome, if provided.
        
        Main results are in CSV files. Three CSV files contain respectively results for reads that have fragsments coming from the first reference only, the second reference only or both references. Another CSV file contains headers of reads that did not match anywhere. Finally, three files are produced when using Blast: ``breakpoints.fasta``, containing the breakpoint portions to Blast, ``res_blast.csv`` containing the result of Blast on ``breakpoints.csv`` and ``compressed.fasta``, a compressed version of ``res_blast.csv`` keeping only results of the best e-value/bit-score for each input sequences and produce a fasta-like file.
        
        FRAGS follows the standards for software development with continuous integration on Gitlab (https://gitlab.pasteur.fr/nmaillet/frags) and automatic on-line documentation (https://frags.readthedocs.io/en/latest/).
        
        
        
        Installation
        ============
        
        In order to install FRAGS, you can use **pip**:
        
        .. code-block:: shell
        
            pip3 install frags
        
        This command installs FRAGS and its Python dependencies.
        
        
        Usage
        =====
        
        From the command line:
        
        .. code-block:: shell
        
            frags --help
        
Keywords: reads,recombination,chimeric,virus,genomes
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.7
Provides-Extra: test
