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            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "beast2\\_constsites: Update BEAST2 XML to account for constant sites\n===================================================================\n\n|Build Status|\n\nIntroduction\n------------\n\nBased on this\n`suggestion <https://groups.google.com/forum/#!topic/beast-users/QfBHMOqImFE>`__\nby Remco, we can correctly account for constant sites in a BEAST2\nanalysis by adding the following ``data`` tag below your current\n``data`` tag:\n\n::\n\n    <data id=\"xyz\" spec=\"FilteredAlignment\" filter=\"-\" data=\"@xyzOriginal\" constantSiteWeights=\"100 200 300 400\"/>\n\nThis assumes that your original ``<data>`` tag had ``id=xyz`` and was\nrenamed to ``id=xyzOriginal``, and that you have 1000 constant sites\nthat were removed from the alignment, with:\n\n-  100 As\n-  200 Cs\n-  300 Gs\n-  400 Ts\n\nWhat does this do?\n------------------\n\nThis script will take a FASTA file with a single DNA sequence (e.g., a\nbacterial chromosome), a VCF file containing the position of SNPs along\nthe FASTA file (e.g., as outputted from\n`snippy-core <https://www.github.com/tseemann/snippy>`__) and the XML\nfile produced by BEAUTi containing only variable sites. It will output a\nnew XML file named ``<original_xml_name>_plus_const.xml`` with the added\ninformation to account for constant sites. There is nothing else you\nneed to do but run BEAST2.\n\nIt will optionally also take a BED file with positions to mask (e.g.,\npositions of phage).\n\nHow to install?\n---------------\n\n::\n\n    pip3 install b2constsites\n\nHow to run it?\n--------------\n\nIf installed correctly, a scripted called ``run_b2cs`` should be\navailable in your path:\n\n::\n\n    run_b2cs --help\n\nAt a minimum, you need to supply a sequence file with your reference\n(assuming it has a single chromosome entry --- this was designed for\nbacterial genomics, but may work with viral too), a VCF file with\nvariants, and the XML output from BEAUTi.\n\n::\n\n    run_b2cs myref.fasta myvar.vcf myxml.xml\n\nA new file called ``myxml_plus_const.xml`` will be created in the same\nfolder as ``myxml.xml``.\n\nASSUMPTIONS and CAVEATS\n-----------------------\n\nThis script will:\n\n-  Only take in to account SNPs and MNPs annotated in the VCF. Other\n   variant types will be ignored.\n-  Will only take into consideration A, C, G, and T bases in your\n   reference sequence. All other characters will be ignored.\n-  Has not been tested with BEAST1.8, and as far as I know it will\n   **not** work with that version of BEAST. This was designed for use\n   with BEAST2.\n\nThe output will be, therefore, an approximation. However, it should be a\nclose enough approximation that it will provide a better inference from\nBEAST2 than if one uses only variable sites, and then corrects in some\n*post hoc* manner.\n\nAuthors\n-------\n\n| Anders Gon\u00e7alves da Silva\n| Sarah Baines\n| Jean Lee\n| Torsten Seemann\n\nMaintainer\n----------\n\nAnders Gon\u00e7alves da Silva\n\nIssues or Questions\n-------------------\n\n`GitHub Issues <https://github.com/andersgs/beast2_constsites/issues>`__\n\n.. |Build Status| image:: https://travis-ci.org/andersgs/beast2_constsites.svg?branch=master\n   :target: https://travis-ci.org/andersgs/beast2_constsites\n",
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