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        "author": "Guanliang Meng",
        "author_email": "mengguanliang@foxmail.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": "# msa_cigars\n\n## 1 Introduction\n\n`msa_cigars` is a tool to get the CIGARs of a multiple sequence alignment. ONE alignment in the input file is assumed! CIGARs are in respect of the reference sequence. By Guanliang MENG, see https://github.com/linzhi2013/msa_cigars. \n\n## 2 Installation\n\n    pip install msa_cigars\n\nThere will be a command `msa_cigars` created under the same directory as your `pip` command.\n\n## 3 Usage\n    \n    $ msa_cigars\n    usage: msa_cigars [-h] -i <FILE> -refseq_id <STR> [-n <STR>] [-g <STR>]\n                     [-f <FORMAT>] [-o <FILE>]\n\n        To get the CIGARs of a multiple sequence alignment.\n        ONE alignment in the input file is assumed!\n\n        CIGARs are in respect of the reference sequence.\n\n        'O' normal bases, e.g. A, T, G, C\n        '-' deletion\n        'N' unknown base\n\n            seq - - - N N N O O O\n         refseq - N O N - O O N -\n          cigar P n D B u U M N I\n\n        By Guanliang MENG,\n        see https://github.com/linzhi2013/msa_cigars.\n\n        optional arguments:\n          -h, --help        show this help message and exit\n          -i <FILE>         input msa file\n          -refseq_id <STR>  MsaCigars class uses regular expression to find out the\n                            sequence id of refseq. Thus, make sure the value of\n                            'refseq_id' option is unique among the input msa file.\n          -n <STR>          character of unknown base [N]\n          -g <STR>          character of gap base [-]\n          -f <FORMAT>       the msa format [fasta]\n          -o <FILE>         outfile name [stdout]\n\n\n## 4 Author\nGuanliang MENG\n\n## 5 Citation\nCurrently I have no plan to publish `msa_cigars`.\n\nHowever, since `msa_cigars` makes use of `Biopython`, you should also cite it if you use `breakSeqInNs_then_translate` 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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        "name": "msa-cigars",
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        "summary": "To return CIGAR strings of a multiple sequences alignment",
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