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    "info": {
        "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": "# breakSeqInNs_then_translate\n\n## 1 Introduction\n\n`breakSeqInNs_then_translate` is a tool to filter the sequences by translating the protein coding genes (PCGs) with proper genetic code table, if one of the PCGs has interal stop codon, filter out this sequence. By Guanliang MENG, see https://github.com/linzhi2013/breakSeqInNs_then_translate.\n\n## 2 Installation\n\n    pip install breakSeqInNs_then_translate\n\nThere will be a command `breakSeqInNs_then_translate` created under the same directory as your `pip` command.\n\n## 3 Usage\n    \n    $ breakSeqInNs_then_translate\n    usage: breakSeqInNs_then_translate.py [-h] [-seq <seq>] [-seqfile <file>]\n                                          [-seqformat {fa,gb}] [-code <int>] [-nb]\n                                          [-gb_genes <int>] [-maxStopGenes <int>]\n\n    Filter the sequences by translating the protein coding genes (PCGs) with\n    proper genetic code table, if one of the PCGs has interal stop codon, filter\n    out this sequence. Beware: if the seq has Ns, then this script will translate\n    the sub seqs with three frames (0, 1, 2), only when all these three kinds of\n    frames have interal stopCodon the seq will be treated as have InternalStop!.\n    By Guanliang MENG, see\n    https://github.com/linzhi2013/breakSeqInNs_then_translate\n\n    optional arguments:\n      -h, --help           show this help message and exit\n      -seq <seq>           input sequence\n      -seqfile <file>      input fasta or genbank file\n      -seqformat {fa,gb}   input -seqfile format [fa]\n      -code <int>          genetic code table [1]\n      -nb                  do not break sequence in Ns when translate [break]\n      -gb_genes <int>      if a genbank record has no less than -gb_genes PCGs and\n                           no more than -maxStopGenes PCGs has InternalStops, we\n                           keep this record. But if a genbank record has less than\n                           -gb_genes PCGs, then we will discard this record if any\n                           of its PCGs has InternalStops. This is because we may\n                           want to tolerate some assembly/sequencing errors. This\n                           has no effect on fasta input file. [5]\n      -maxStopGenes <int>  the maximum number of PCGs can have InternalStops in a\n                           genbank record if do not discard it [0]\n\n\n## 4 Author\nGuanliang MENG\n\n## 5 Citation\nCurrently I have no plan to publish `breakSeqInNs_then_translate`.\n\nHowever, since `breakSeqInNs_then_translate` 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": "breakSeqInNs-then-translate",
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        "summary": "To filter the sequences by translating the protein coding genes (PCGs) with proper genetic code table, if one of the PCGs has interal stop codon, filter out this sequence. See https://github.com/linzhi2013/breakSeqInNs_then_translate",
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