{ "info": { "author": "Mike Halagan", "author_email": "mhalagan@nmdp.org", "bugtrack_url": null, "classifiers": [ "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)", "Natural Language :: English", "Programming Language :: Python :: 3.6" ], "description": "===============================\npyHML\n===============================\n\n\n.. image:: https://img.shields.io/travis/nmdp-bioinformatics/pyHML.svg\n :target: https://travis-ci.org/nmdp-bioinformatics/pyHML\n\n.. image:: https://readthedocs.org/projects/pyhml/badge/?version=latest\n :target: https://pyhml.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. image:: https://pyup.io/repos/github/nmdp-bioinformatics/pyHML/shield.svg\n :target: https://pyup.io/repos/github/nmdp-bioinformatics/pyHML/\n :alt: Updates\n\n.. image:: https://img.shields.io/pypi/v/pyhml.svg\n :target: https://pypi.python.org/pypi/pyhml\n\n.. image:: https://coveralls.io/repos/github/nmdp-bioinformatics/pyHML/badge.svg?branch=master\n\t\t:target: https://coveralls.io/github/nmdp-bioinformatics/pyHML?branch=master\n\n\n\nPython HML parser\n\n* Free software: LGPL 3.0\n* Documentation: https://pyhml.readthedocs.io.\n* `Jupyter Notebook`_\n\nFeatures\n--------\n\n.. code-block:: python3\n\n import pyhml\n hml_file = \"hml_example.xml\"\n hmlparser = pyhml.HmlParser()\n hml = hmlparser.parse(hml_file)\n outdir = 'output/directory'\n\n # Print out each subject in fasta format\n hml.tobiotype(outdir, dtype='fasta', by='subject')\n\n # Print out the full HML file in IMGT dat file format\n hml.tobiotype(outdir, dtype='imgt', by='file')\n\n # Get pandas DF from HML object\n pandasdf = hml.toPandas()\n print(pandasdf)\n\n ID Locus glstring dbversion \\\n\t0 1367-7150-8 HLA-A HLA-A*01:01:01+HLA-A*24:02:01 3.14.0 \n\t1 1367-7150-8 HLA-A HLA-A*01:01:01+HLA-A*24:02:01 3.14.0 \n\t2 1367-7150-8 HLA-A HLA-A*01:01:01+HLA-A*24:02:01 3.14.0 \n\t3 1367-7150-8 HLA-A HLA-A*01:01:01+HLA-A*24:02:01 3.14.0 \n\t4 1367-7150-8 HLA-B HLA-B*08:01:01+HLA-B*57:01:01 3.14.0 \n\t5 1367-7150-8 HLA-B HLA-B*08:01:01+HLA-B*57:01:01 3.14.0 \n\t6 1367-7150-8 HLA-B HLA-B*08:01:01+HLA-B*57:01:01 3.14.0 \n\t7 1367-7150-8 HLA-B HLA-B*08:01:01+HLA-B*57:01:01 3.14.0 \n\t8 1367-7150-8 HLA-C HLA-C*06:02:01+HLA-C*07:01:01 3.14.0 \n\t9 1367-7150-8 HLA-C HLA-C*06:02:01+HLA-C*07:01:01 3.14.0 \n\t10 1367-7150-8 HLA-C HLA-C*06:02:01+HLA-C*07:01:01 3.14.0 \n\t11 1367-7150-8 HLA-C HLA-C*06:02:01+HLA-C*07:01:01 3.14.0 \n\t12 1367-7150-8 HLA-DPB1 HLA-DPB1*02:01:02+HLA-DPB1*04:01:01 3.14.0 \n\t13 1367-7150-8 HLA-DPB1 HLA-DPB1*02:01:02+HLA-DPB1*04:01:01 3.14.0 \n\t14 1367-7150-8 HLA-DRB1 HLA-DRB1*03:01:01+HLA-DRB1*07:01:01 3.15.0 \n\t15 1367-7150-8 HLA-DRB1 HLA-DRB1*03:01:01+HLA-DRB1*07:01:01 3.15.0 \n\n\t sequence \n\t0 TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGT... \n\t1 TTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCT... \n\t2 TTCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGT... \n\t3 GTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCA... \n\t4 CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTG... \n\t5 GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGG... \n\t6 CCATGGTGAGTTTCCCTGTACAAGAGTCCAAGGGGAGAGGTAAGTG... \n\t7 GGCCTCTGCGGAGAGGAGCGAGGGGCCCGCCCGGCGAGGGCGCAGG... \n\t8 AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTC... \n\t9 CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAA... \n\t10 AGGGATCAGGACGAAGTCCCAGGTCCCGGACGGGGCTCTCAGGGTC... \n\t11 CGCATCCCCACTTCCCACTCCCATTGGGTGTCGGATATCTAGAGAA... \n\t12 CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT... \n\t13 CCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATTGGCCAATT... \n\t14 CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA... \n\t15 CATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA... \n\n\nInstall\n--------\n\n.. code-block:: bash\n\n pip install pyhml\n\n\nCredits\n---------\n\nThis package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.\n\n.. _Cookiecutter: https://github.com/audreyr/cookiecutter\n.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage\n.. _`Jupyter Notebook`: https://github.com/nmdp-bioinformatics/pyHML/blob/master/notebook/Examples.ipynb\n\n\n=======\nHistory\n=======\n\n0.0.5 (2017-04-16)\n------------------\n\n* Improved documentation\n* Fixed issues with parsing HML files with NMDP-CORRECTION\n\n0.0.4 (2017-04-15)\n------------------\n\n* Fixed dependency issues.\n* Moved tobiotype to HML object.\n* Moved toDF to HML object and renamed toPandas()\n* Added tests and linked to travis.ci\n\n0.0.3 (2017-04-14)\n------------------\n\n* Added the ability to parse .gz files\n* Added the ability to parse HML files with bad tags.\n\n\n0.0.2 (2017-11-14)\n------------------\n\n* Fixed issues with parsing HML files with missing data\n\n\n0.0.1 (2017-10-19)\n------------------\n\n* First release on PyPI.\n\n\n", "description_content_type": "", "docs_url": null, "download_url": "", 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