Metadata-Version: 1.1
Name: clsify
Version: 0.1.1
Summary: Classify C. Liberibacter solanacearum haplotypes
Home-page: https://github.com/holtgrewe/clsify
Author: Manuel Holtgrewe
Author-email: manuel.holtgrewe@bihealth.de
License: MIT license
Description: ======
        CLSify
        ======
        
        Classification of *Candidatus Liberibacter solanacearum* following IPPC (International Plant Protection Convention) standard `DP 21: Candidatus Liberibacter solanacearum <https://www.ippc.int/en/publications/84157>`_.
        
        -----------
        Quick Facts
        -----------
        
        - License: MIT
        - Programming Language Python
        
        ------------------------------
        Input / Output - What it Does!
        ------------------------------
        
        This program takes as the input Sanger sequences from the 16S, 16S-23S, and 50S primers from the IPPC standard DP21.
        It then aligns them to the GenBank reference sequences ``EU812559`` and ``EU834131`` (as specified in DP21).
        Based on the alignments and the document DP21, sequence identity is computed and haplotyping is performed, yielding:
        
        - sequence identity to ``EU822559`` for identifying the species *C. Liberibacter solanacearum*, and
        - haplotyping of the read based on variation from the reference sequence.
        
        Sample names can be inferred from the read names or from a separate mapping TSV file.
        
        -----------
        Quick Start
        -----------
        
        This is gonna be really quick!
        
        Installation
        ============
        
        We recommend using `Bioconda <https://bioconda.github.io>`_.
        
        First `install Bioconda <https://bioconda.github.io/user/install.html#getting-started>`_.
        Then:
        
        .. code-block:: bash
        
            # conda install -y clsify
        
        And -- tadaa -- you're ready to go!
        
        Running
        =======
        
        You can have one FASTA (or FASTQ) file with all of your reads or one file for each.
        If you have a single sequence per FASTA (or FASTQ) file then you can use the file name instead of the sequence name.
        
        .. code-block:: bash
        
            # clsify -o result.tsv INPUT.fasta
            ## OR
            # clsify [--use-file-name] -o result.tsv INPUT1.fasta INPUT2.fasta [...]
            ## e.g.,
            # clsify [--use-file-name] -o result.tsv INPUT*.fasta
        
        
        =======
        History
        =======
        
        ------
        v0.1.1
        ------
        
        - Zapping gremlins in haplotype table.
        - Change formatting of README.
        
        ------
        v0.1.0
        ------
        
        Initial release.
        
        - Everything is new!
        
Keywords: clsify
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
