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        "author": "Guanliang Meng",
        "author_email": "linzhi2012@gmail.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "# extract-codon-alignment\n\n## 1 Introduction\n\n`extract-codon-alignment`  (https://github.com/linzhi2013/extract_codon_alignment) is a tool to extract some codon positions (1st, 2nd, 3rd) from a CDS alignment with `Biopython` (http://www.biopython.org/)\n\n## 2 Installation\n\n    $ pip install extract-codon-alignment\n    # or with Bioconda\n    conda install extract-codon-alignment\n\nThere will be a command `extract_codon_alignment` created under the same directory as your `pip` command.\n\n## 3 Usage\n\n    $ extract_codon_alignment\n    usage: extract_codon_alignment [-h] --alignedCDS <file>\n                                   [--aln_format <format>]\n                                   [--codonPoses {1,2,3,12,13,23}] --outAln <file>\n\n    To extract some codon positions (1st, 2nd, 3rd) from a CDS alignment.\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      --alignedCDS <file>   The CDS alignment.\n      --aln_format <format>\n                            the file format for the CDS alignment. Anything\n                            accepted by BioPython is fine [fasta]\n      --codonPoses {1,2,3,12,13,23}\n                            Codon position(s) to be extracted [12]\n      --outAln <file>       output file name\n\n## Author\nGuanliang MENG\n\n## Citation\nCurrently I have no plan to publish `extract-codon-alignment`.\n\nHowever, since `extract-codon-alignment` makes use of `Biopython`, you should cite it if you use `extract-codon-alignment` in your work:\n\n    Peter J. A. Cock, Tiago Antao, Jeffrey T. Chang, Brad A. Chapman, Cymon J. Cox, Andrew Dalke, Iddo Friedberg, Thomas Hamelryck, Frank Kauff, Bartek Wilczynski, Michiel J. L. de Hoon: \u201cBiopython: freely available Python tools for computational molecular biology and bioinformatics\u201d. Bioinformatics 25 (11), 1422\u20131423 (2009). https://doi.org/10.1093/bioinformatics/btp163\n\nPlease go to `http://www.biopython.org/` for more details.",
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