{
    "info": {
        "author": "NMDP Bioinformatics, CIBMTR",
        "author_email": "cibmtr-pypi@nmdp.org",
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        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
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            "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
            "Natural Language :: English",
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        "description": "===============================\nSeqAnn\n===============================\n\n\n.. image:: https://img.shields.io/travis/nmdp-bioinformatics/SeqAnn.svg\n        :target: https://travis-ci.org/nmdp-bioinformatics/SeqAnn\n\n.. image:: https://readthedocs.org/projects/seqann/badge/?version=latest\n        :target: https://seqann.readthedocs.io/en/latest/?badge=latest\n        :alt: Documentation Status\n\n.. image:: https://pyup.io/repos/github/nmdp-bioinformatics/SeqAnn/shield.svg\n     :target: https://pyup.io/repos/github/nmdp-bioinformatics/SeqAnn/\n     :alt: Updates\n\n.. image:: https://img.shields.io/pypi/v/seqann.svg\n        :target: https://pypi.python.org/pypi/seqann\n\n.. image:: https://coveralls.io/repos/github/nmdp-bioinformatics/SeqAnn/badge.svg?branch=master\n        :target: https://coveralls.io/github/nmdp-bioinformatics/SeqAnn?branch=master\n\n\nPython package for annotating gene features\n\n\n* Free software: LGPL 3.0\n* Documentation: https://seqann.readthedocs.io.\n* `Jupyter Notebook`_\n\n\nOverview\n---------\n\nThe ``seqann`` package allows \nusers to annotate gene features in consensus sequences. Annotations can be created by passing consensus sequences to the ``annotate`` method in the\n``BioSeqAnn`` class. No parameters are required when initalizing a ``BioSeqAnn`` class. However, annotations can be\ncreated significantly faster when using a BioSQL database. When a BioSQL database is not provided the lastest `hla.dat`_ file is downloaded and parsed.\nA BioSQL database containing all of IPD-IMGT/HLA is available on DockerHub_ and can be\nrun on any machine that has docker installed. \n\nParameters\n----------\n\nBelow are the list of parameters and the default values used when initalizing a ``BioSeqAnn`` object.\n\n.. table::\n    :widths: 10 10 10 50\n\n    +-------------+-------------------+---------+-------------------------------------------------------------------------------+\n    | Parameter   | Type              | Default | Description                                                                   |\n    +=============+===================+=========+===============================================================================+\n    | server      | ``BioSeqDatabase``| None    | A BioSQL database containing all of the sequence data from IPD-IMGT/HLA.      |\n    +-------------+-------------------+---------+-------------------------------------------------------------------------------+\n    | dbversion   | ``str``           | Latest  | The IPD-IMGT/HLA or KIR database release.                                     |\n    +-------------+-------------------+---------+-------------------------------------------------------------------------------+\n    | datfile     | ``str``           | None    | The IPD-IMGT/HLA or KIR dat file to use in place of the **server** parameter. |\n    +-------------+-------------------+---------+-------------------------------------------------------------------------------+\n    | kir         | ``bool``          | False   | Flag for indicating the input sequences are from the KIR gene system.         |\n    +-------------+-------------------+---------+-------------------------------------------------------------------------------+\n    | align       | ``bool``          | False   | Flag for producing the alignments along with the annotations.                 |\n    +-------------+-------------------+---------+-------------------------------------------------------------------------------+\n    | verbose     | ``bool``          | False   | Flag for running in verbose mode.                                             |\n    +-------------+-------------------+---------+-------------------------------------------------------------------------------+\n    | verbosity   | ``int``           | None    | Numerical value to indicate how verbose the output will be in verbose mode.   |\n    +-------------+-------------------+---------+-------------------------------------------------------------------------------+\n    | debug       | ``Dict``          | None    | A dictionary containing a process names as the key and verbosity as the value |\n    +-------------+-------------------+---------+-------------------------------------------------------------------------------+\n\nUsage\n---------\n\nTo annotated a sequence initialize a new ``BioSeqAnn`` object and then pass the sequence to the\n``annotate`` method. The sequence must be a Biopython ``Seq``. The locus of the sequence is not required but it will improve the accuracy of the annotation.\n\n\n  The packages `ncbi-blast+` and `clustalo` are required to be installed on your system.\n\n\n.. code-block:: python3\n\n    from seqann import BioSeqAnn\n    seqann = BioSeqAnn()\n    ann = seqann.annotate(sequence, \"HLA-A\")\n\n\nThe annotation of sequence can be done with or without providing a ``BioSeqDatabase``. To use a BioSQL database \ninitialize a ``BioSeqDatabase`` with the parameters that match the database you have running. If you are \nrunning the imgt_biosqldb from DockerHub_ then the following parameters we be the same. \n\n.. code-block:: python3\n\n    from seqann import BioSeqAnn\n    from BioSQL import BioSeqDatabase\n    server = BioSeqDatabase.open_database(driver=\"pymysql\", user=\"root\",\n                                          passwd=\"my-secret-pw\", host=\"localhost\",\n                                          db=\"bioseqdb\", port=3306)\n    seqann = BioSeqAnn(server=server)\n    ann = seqann.annotate(sequence, \"HLA-A\")\n\n\nYou may need to set environment variables: *BIOSQLHOST* (e.g. \"localhost\") and *BIOSQLPORT*  (e.g. 3306)  to your docker instance.\n\n\nAnnotations\n------------\n\n.. code-block:: shell\n\n            {\n                 'complete_annotation': True,\n                 'annotation': {'exon_1': SeqRecord(seq=Seq('AGAGACTCTCCCG', SingleLetterAlphabet()), id='HLA:HLA00630', name='HLA:HLA00630', description='HLA:HLA00630 DQB1*03:04:01 597 bp', dbxrefs=[]),\n                                'exon_2': SeqRecord(seq=Seq('AGGATTTCGTGTACCAGTTTAAGGCCATGTGCTACTTCACCAACGGGACGGAGC...GAG', SingleLetterAlphabet()), id='HLA:HLA00630', name='HLA:HLA00630', description='HLA:HLA00630 DQB1*03:04:01 597 bp', dbxrefs=[]),\n                                'exon_3': SeqRecord(seq=Seq('TGGAGCCCACAGTGACCATCTCCCCATCCAGGACAGAGGCCCTCAACCACCACA...ATG', SingleLetterAlphabet()), id='HLA:HLA00630', name='<unknown name>', description='HLA:HLA00630', dbxrefs=[])},\n                 'features': {'exon_1': SeqFeature(FeatureLocation(ExactPosition(0), ExactPosition(13), strand=1), type='exon_1'),\n                              'exon_2': SeqFeature(FeatureLocation(ExactPosition(13), ExactPosition(283), strand=1), type='exon_2')\n                              'exon_3': SeqFeature(FeatureLocation(ExactPosition(283), ExactPosition(503), strand=1), type='exon_3')},\n                 'method': 'nt_search and clustalo',\n                 'gfe': 'HLA-Aw2-1-1-1-1-1-1-1-1-1-1-1-1-1-1-1-4',\n                 'seq': SeqRecord(seq=Seq('AGAGACTCTCCCGAGGATTTCGTGTACCAGTTTAAGGCCATGTGCTACTTCACC...ATG', SingleLetterAlphabet()), id='HLA:HLA00630', name='HLA:HLA00630', description='HLA:HLA00630 DQB1*03:04:01 597 bp', dbxrefs=[])\n            }\n\n\nOnce a sequence has been annotated the gene features and their corresponding sequences are available in the returned ``Annotation`` object. If a full\nannotation is not able to be produced then nothing will be returned. Below is an example showing how the features can be accessed and printed out.\n\n.. code-block:: python3\n\n    ann = seqann.annotate(sequence, \"HLA-A\")\n    for feat in ann.annotation:\n        print(feat, ann.gfe, str(ann.annotation[feat].seq), sep=\"\\t\")\n\n\nInstall\n------------\n\n.. code-block:: shell\n\n    pip install seqann\n\n\nDependencies\n------------\n* `Clustal Omega`_ 1.2.0 or higher\n* `Python 3.6`_\n* blastn_\n\n.. _DockerHub: https://hub.docker.com/r/nmdpbioinformatics/imgt_biosqldb/\n.. _`GitHub page`: http://google.com\n.. _`hla.dat`: https://github.com/ANHIG/IMGTHLA\n.. _`Python 3.6`: https://www.python.org/downloads\n.. _`Clustal Omega`: http://www.clustal.org/omega/\n.. _blastn: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _`Jupyter Notebook`: https://github.com/nmdp-bioinformatics/SeqAnn/blob/master/notebook/Examples.ipynb\n\n\n",
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