{ "info": { "author": "Manuel Holtgrewe", "author_email": "manuel.holtgrewe@bihealth.de", "bugtrack_url": null, "classifiers": [ "Development Status :: 2 - Pre-Alpha", "Intended Audience :: Developers", "License :: OSI Approved :: MIT License", "Natural Language :: English", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8" ], "description": "======\nCLSify\n======\n\nClassification of *Candidatus Liberibacter solanacearum* following IPPC (International Plant Protection Convention) standard `DP 21: Candidatus Liberibacter solanacearum `_.\n\n-----------\nQuick Facts\n-----------\n\n- License: MIT\n- Programming Language Python\n\n------------------------------\nInput / Output - What it Does!\n------------------------------\n\nThis program takes as the input Sanger sequences from the 16S, 16S-23S, and 50S primers from the IPPC standard DP21.\nIt then aligns them to the GenBank reference sequences ``EU812559`` and ``EU834131`` (as specified in DP21).\nBased on the alignments and the document DP21, sequence identity is computed and haplotyping is performed, yielding:\n\n- sequence identity to ``EU822559`` for identifying the species *C. Liberibacter solanacearum*, and\n- haplotyping of the read based on variation from the reference sequence.\n\nSample names can be inferred from the read names or from a separate mapping TSV file.\n\n-----------\nQuick Start\n-----------\n\nThis is gonna be really quick!\n\nInstallation\n============\n\nWe recommend using `Bioconda `_.\n\nFirst `install Bioconda `_.\nThen:\n\n.. code-block:: bash\n\n # conda install -y clsify\n\nAnd -- tadaa -- you're ready to go!\n\nRunning\n=======\n\nYou can have one FASTA (or FASTQ) file with all of your reads or one file for each.\nIf you have a single sequence per FASTA (or FASTQ) file then you can use the file name instead of the sequence name.\n\n.. code-block:: bash\n\n # clsify -o result.tsv INPUT.fasta\n ## OR\n # clsify [--use-file-name] -o result.tsv INPUT1.fasta INPUT2.fasta [...]\n ## e.g.,\n # clsify [--use-file-name] -o result.tsv INPUT*.fasta\n\n\n=======\nHistory\n=======\n\n------\nv0.1.1\n------\n\n- Zapping gremlins in haplotype table.\n- Change formatting of README.\n\n------\nv0.1.0\n------\n\nInitial release.\n\n- Everything is new!", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/holtgrewe/clsify", "keywords": "clsify", "license": "MIT license", "maintainer": "", "maintainer_email": "", "name": "clsify", "package_url": "https://pypi.org/project/clsify/", "platform": "", "project_url": "https://pypi.org/project/clsify/", "project_urls": { "Homepage": "https://github.com/holtgrewe/clsify" }, "release_url": "https://pypi.org/project/clsify/0.1.1/", "requires_dist": null, "requires_python": "", "summary": "Classify C. 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