{
    "info": {
        "author": "Han Lin",
        "author_email": "hotdogee@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: BSD License",
            "Natural Language :: English",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.6",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
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        "description": "===============================\ngff3-py\n===============================\n\n.. image:: https://travis-ci.org/hsiaoyi0504/gff3-py.svg?branch=master\n    :target: https://travis-ci.org/hsiaoyi0504/gff3-py\n\n\nManipulate genomic features and validate the syntax and reference sequence of your |GFF3|_ files.\n\n* Free software: NAL Public Domain License\n* Documentation: https://gff3-py.readthedocs.org.\n\nFeatures\n--------\n\n* **Simple data structures**: Parses a |GFF3|_ file into a structure composed of simple python |dict|_ and |list|_.\n* **Validation**: Validates the |GFF3|_ syntax on parse, and saves the error messages in the parsed structure.\n* **Best effort parsing**: Despite any detected errors, continue to parse the whole file and make as much sense to it as possible.\n* Uses the python |logging|_ library to log error messages with support for custom loggers.\n* Parses embeded or external |FASTA|_ sequences to check bounds and number of ``N`` s.\n* Check and correct the phase for ``CDS`` features.\n* Tree traversal methods ``ancestors`` and ``descendants`` returns a simple ``list`` in Breadth-first search order.\n* Transfer children and parents using the ``adopt`` and ``adopted`` methods.\n* Test for overlapping features using the ``overlap`` method.\n* Remove a feature and its associated features using the ``remove`` method.\n* Write the modified structure to a GFF3 file using the ``write`` mthod.\n\nQuick Start\n-----------\n\nAn example that just parses a GFF3 file named ``annotations.gff`` and validates it \nusing an external FASTA file named ``annotations.fa`` looks like:\n\n.. code:: python\n\n    # validate.py\n    # ============\n    from gff3 import Gff3\n\n    # initialize a Gff3 object\n    gff = Gff3()\n    # parse GFF3 file and do syntax checking, this populates gff.lines and gff.features\n    # if an embedded ##FASTA directive is found, parse the sequences into gff.fasta_embedded\n    gff.parse('annotations.gff')\n    # parse the external FASTA file into gff.fasta_external\n    gff.parse_fasta_external('annotations.fa')\n    # Check seqid, bounds and the number of Ns in each feature using one or more reference sources\n    gff.check_reference(allowed_num_of_n=0, feature_types=['CDS'])\n    # Checks whether child features are within the coordinate boundaries of parent features\n    gff.check_parent_boundary()\n    # Calculates the correct phase and checks if it matches the given phase for CDS features\n    gff.check_phase()\n    \nA more feature complete GFF3 validator with a command line interface which also generates validation\nreport in MarkDown is available under ``examples/gff_valid.py``\n\nThe following example demonstrates how to filter, tranverse, and modify the parsed gff3 ``lines`` list.\n\n1. Change features with type ``exon`` to ``pseudogenic_exon`` and type ``transcript`` to ``pseudogenic_transcript`` if the feature has an ancestor of type ``pseudogene``\n\n2. If a ``pseudogene`` feature overlaps with a ``gene`` feature, move all of the children from the ``pseudogene`` feature to the ``gene`` feature, and remove the ``pseudogene`` feature.\n\n.. code:: python\n\n    # fix_pseudogene.py\n    # =================\n    from gff3 import Gff3\n    gff = Gff3('annotations.gff')\n    type_map = {'exon': 'pseudogenic_exon', 'transcript': 'pseudogenic_transcript'}\n    pseudogenes = [line for line in gff.lines if line['line_type'] == 'feature' and line['type'] == 'pseudogene']\n    for pseudogene in pseudogenes:\n        # convert types\n        for line in gff.descendants(pseudogene):\n            if line['type'] in type_map:\n                line['type'] = type_map[line['type']]\n        # find overlapping gene\n        overlapping_genes = [line for line in gff.lines if line['line_type'] == 'feature' and line['type'] == 'gene' and gff.overlap(line, pseudogene)]\n        if overlapping_genes:\n            # move pseudogene children to overlapping gene\n            gff.adopt(pseudogene, overlapping_genes[0])\n            # remove pseudogene\n            gff.remove(pseudogene)\n    gff.write('annotations_fixed.gff')\n\n.. |GFF3| replace:: ``GFF3``\n.. |dict| replace:: ``dict``\n.. |list| replace:: ``list``\n.. |logging| replace:: ``logging``\n.. |FASTA| replace:: ``FASTA``\n\n.. _GFF3: http://www.sequenceontology.org/gff3.shtml\n.. _dict: https://docs.python.org/2/tutorial/datastructures.html#dictionaries\n.. _list: https://docs.python.org/2/tutorial/datastructures.html#more-on-lists\n.. _logging: https://docs.python.org/2/library/logging.html\n.. _FASTA: http://en.wikipedia.org/wiki/FASTA_format\n\n\n\n\nHistory\n-------\n\n\n\n1.0.0 (2018-12-01)\n---------------------\n\n* Fix python3 problem\n* Added sequence functions: complement(seq) and translate(seq)\n* Added fasta write function: fasta_dict_to_file(fasta_dict, fasta_file, line_char_limit=None)\n* Added Gff method to return the sequence of line_data: sequence(self, line_data, child_type=None, reference=None)\n* Gff.write no longer prints redundent '###' when the whole gene is marked as removed\n\n\n0.3.0 (2015-03-10)\n---------------------\n\n* Fixed phase checking.\n\n0.2.0 (2015-01-28)\n---------------------\n\n* Supports python 2.6, 2.7, 3.3, 3.4, pypy.\n* Don't report empty attributes as errors.\n* Improved documentation.\n\n0.1.0 (2014-12-11)\n---------------------\n\n* First release on PyPI.",
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