semvec/pypi-packages huggingface dataset:
clsify 0.1.1
Classify C. Liberibacter solanacearum haplotypes
License: MIT license
Keywords: clsify

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CLSify
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Classification of *Candidatus Liberibacter solanacearum* following IPPC (International Plant Protection Convention) standard `DP 21: Candidatus Liberibacter solanacearum <https://www.ippc.int/en/publications/84157>`_.

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Quick Facts
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- License: MIT
- Programming Language Python

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Input / Output - What it Does!
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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.

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Quick Start
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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
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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


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History
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v0.1.1
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- Zapping gremlins in haplotype table.
- Change formatting of README.

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v0.1.0
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Initial release.

- Everything is new!