Metadata-Version: 1.2
Name: xlavir
Version: 0.4.0
Summary: Excel report from viral sequencing analysis output
Home-page: https://github.com/peterk87/xlavir
Author: Peter Kruczkiewicz
Author-email: peter.kruczkiewicz@gmail.com
License: MIT license
Description: ======
        xlavir
        ======
        
        
        .. image:: https://img.shields.io/pypi/v/xlavir.svg
                :target: https://pypi.python.org/pypi/xlavir
        
        .. image:: https://github.com/peterk87/xlavir/workflows/CI/badge.svg?branch=master
                :target: https://github.com/peterk87/xlavir/actions
        
        .. image:: https://readthedocs.org/projects/xlavir/badge/?version=latest
                :target: https://xlavir.readthedocs.io/en/latest/?badge=latest
                :alt: Documentation Status
        
        
        Excel report from viral sequencing data analysis output from the `nf-core/viralrecon`_ or `peterk87/nf-virontus`_ Nextflow pipelines.
        
        
        * Free software: MIT license
        * Documentation: https://xlavir.readthedocs.io.
        
        
        Features
        --------
        
        * Collect sample results from a `nf-core/viralrecon`_ or `peterk87/nf-virontus`_ into a Excel report
            * Samtools_ read mapping stats (``flagstat``)
            * Mosdepth_ read mapping coverage information
            * Variant calling information (SnpEff_ and SnpSift_ results, VCF file information)
            * Consensus sequences
        * QA/QC of sample analysis results (basic PASS/FAIL based on minimum genome coverage and depth)
        * Nextflow workflow execution information
        * Prepend worksheets from other Excel documents into the report (e.g. cover page/sheet, sample sheet, lab results)
        * Add custom images into worksheets with custom names and descriptions (e.g. phylogenetic tree figure PNG)
        
        Roadmap
        -------
        
        * Bcftools_ variant calling stats sheet
        * Sample metadata table to merge with certain stats?
        * YAML config to info sheet?
        * coverage chart with controls?
        
        Credits
        -------
        
        This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        .. _nf-core/viralrecon: https://github.com/nf-core/viralrecon
        .. _peterk87/nf-virontus: https://github.com/peterk87/nf-virontus/
        .. _Bcftools: https://www.htslib.org/doc/bcftools.html
        .. _Samtools: https://samtools.github.io/
        .. _SnpEff: https://pcingola.github.io/SnpEff/se_introduction/
        .. _SnpSift: https://pcingola.github.io/SnpEff/ss_introduction/
        .. _Mosdepth: https://github.com/brentp/mosdepth
        
        
        =======
        History
        =======
        
        0.4.0 (2021-04-23)
        ------------------
        
        * Adds "Variants Summary" sheet summarizing variant information across all samples
        * Adds comments to AF values in "Variant Matrix" sheet
        * Fixes width/height of cell comments to be based on length of comment text
        
        0.3.0 (2021-04-23)
        ------------------
        
        * Adds support for adding Ct values from a Ct values table (tab-delimited, CSV, ODS, XLSX format) into an xlavir report.
        
        0.2.4 (2021-04-19)
        ------------------
        
        * Fixes issue with SnpSift table file parsing and variable naming in variants.py (#4, #5)
        
        0.2.3 (2021-04-19)
        ------------------
        
        * Fixes issue with SnpSift table file parsing. Adds check to see if SnpSift column is dtype object/str before using .str Series methods (#4)
        
        0.2.2 (2021-03-30)
        ------------------
        
        * Fixes issue with SnpEff/SnpSift AA change parsing.
        
        0.2.1 (2021-03-29)
        ------------------
        
        * Fix division by zero error due to variants with DP values of 0
        
        0.2.0 (2021-03-04)
        ------------------
        
        * Added header comments with descriptions of field content
        * Added comment to Variant Matrix sheet A1 cell describing what is shown in the matrix
        * Added highlighting of samples failing QC in other sheets
        * Fixed image scaling by determining image size with imageio
        * Added Medaka_ / Longshot_ VCF parsing
        
        0.1.1 (2021-02-16)
        ------------------
        
        * Collect sample results from a `nf-core/viralrecon`_ or `peterk87/nf-virontus`_ into a Excel report
            * Samtools_ read mapping stats (``flagstat``)
            * Mosdepth_ read mapping coverage information
            * Variant calling information (SnpEff_ and SnpSift_ results, VCF file information)
            * Consensus sequences
        * iVar VCF parsing
        * QA/QC of sample analysis results (basic PASS/FAIL based on minimum genome coverage and depth)
        * Nextflow workflow execution information
        * Prepend worksheets from other Excel documents into the report (e.g. cover page/sheet, sample sheet, lab results)
        * Add custom images into worksheets with custom names and descriptions (e.g. phylogenetic tree figure PNG)
        
        .. _Cookiecutter: https://github.com/audreyr/cookiecutter
        .. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage
        .. _nf-core/viralrecon: https://github.com/nf-core/viralrecon
        .. _peterk87/nf-virontus: https://github.com/peterk87/nf-virontus/
        .. _Bcftools: https://www.htslib.org/doc/bcftools.html
        .. _Samtools: https://samtools.github.io/
        .. _SnpEff: https://pcingola.github.io/SnpEff/se_introduction/
        .. _SnpSift: https://pcingola.github.io/SnpEff/ss_introduction/
        .. _Mosdepth: https://github.com/brentp/mosdepth
        .. _Longshot: https://github.com/pjedge/longshot
        .. _Medaka: https://github.com/nanoporetech/medaka
        
Keywords: xlavir
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Requires-Python: >=3.5
