hlso 0.4.4
Classify C. Liberibacter solanacearum haplotypes
License: MIT license
Keywords: hlso

.. image:: https://readthedocs.org/projects/haplotype-lso/badge/?version=latest
    :target: https://haplotype-lso.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

=============
Haplotype-LSO
=============

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

- `Official Web App <https://haplotype-lso.bihealth.org>`_
- `Tutorial <https://haplotype-lso.readthedocs.io/en/latest/?badge=latest>`_

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Quick Facts
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- License: MIT
- Programming Language Python

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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.

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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 (``clsify`` is the old package name of Haplotype-Lso and it will be renamed soon):

.. 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

    # hlso -o result.tsv INPUT.fasta
    ## OR
    # hlso [--use-file-name] -o result.tsv INPUT1.fasta INPUT2.fasta [...]
    ## e.g.,
    # hlso [--use-file-name] -o result.tsv INPUT*.fasta

---------------
Developer Guide
---------------

Releasing Packages
==================

For the `PyPi package <https://pypi.org/project/hlso/>`_:

.. code-block:: shell

    $ python setup.py sdist
    $ twine upload --repository-url https://test.pypi.org/legacy/ dist/hlso-*.tar.gz
    $ twine upload dist/hlso-*.tar.gz

For the Bioconda package, see `the great documentation <http://bioconda.github.io/updating.html>`_.
The Docker image will automatically be created as a BioContainer when the Bioconda package is built.


=======
History
=======


------
v0.4.4
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- Fix file conversion problem.

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v0.4.3
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- Fixing issue with AB1/SCF support.

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v0.4.2
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- Fix for multi-region sequences.
- Fixing collision, variant must be identified by sequence, position, and reference.

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v0.4.1
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- Fixing bug with display of BLAST match.
- Adding link-out to NCBI WWWBLAST submission.
- Removing some cruft from repository.
- Fixing bug in phylogenetic coputation in case of BLAST all-to-all matches not a square number.

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v0.4.0
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- Compute region-wise phylogenetic tree.

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v0.3.4
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- Support for uploading to PyPi.

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v0.3.3
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- Fixing regular expression.

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v0.3.2
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- Changing file name pattern do dot-separated scheme.
- Greatly extending documentation.

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v0.3.1
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- Starting out with tutorial and manual.

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v0.3.0
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- Adding tutorial.
- Rebranding as "Haplotype-LSO" (``hlso``).
- Properly normalizing indels according to Tan et al. (2015).
- Adding support for haplotyping with indels.

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v0.2.0
------

- Removing dependency on bcftools.
  Haplotyping is done from BLAST match now.
- Adding tests for ``blast`` module.
- Rewrite of the whole BLAST and haplotyping interface and architecture.

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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
------

Initial release.

- Everything is new!