{ "info": { "author": "Simon Greenhill", "author_email": "simon@simon.net.nz", "bugtrack_url": null, "classifiers": [ "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Programming Language :: Python", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering", "Topic :: Scientific/Engineering :: Bio-Informatics", "Topic :: Software Development :: Libraries :: Python Modules" ], "description": "\npython-nexus - Generic nexus (.nex, .trees) reader for python\n=============================================================\n\nReading a Nexus\n---------------\n\n>>> import os\n>>> EXAMPLE_DIR = os.path.join(os.path.dirname(__file__), 'examples')\n>>>\n>>> from nexus import NexusReader\n>>> n = NexusReader()\n>>> n.read_file(os.path.join(EXAMPLE_DIR, 'example.nex'))\n...\n>>> n = NexusReader(os.path.join(EXAMPLE_DIR, 'example.nex'))\n...\n\n# display blocks found in data file\n>>> n.blocks\n{'data': }\n\n`data` blocks\n-------------\n\n>>> n.data.nchar\n2\n\n>>> n.data.ntaxa\n4\n\n>>> n.data.format\n{'datatype': 'standard', 'symbols': '01', 'gap': '-'}\n\n>>> n.data.matrix.keys()\n['Simon', 'Louise', 'Betty', 'Harry']\n\n>>> n.data.matrix['Simon']\n['0', '1']\n\n>>> sorted(n.data.taxa)\n['Betty', 'Harry', 'Louise', 'Simon']\n\n>>> sorted(n.data.matrix.keys())\n['Betty', 'Harry', 'Louise', 'Simon']\n\n>>> for taxon, characters in n.data: #doctest: +SKIP\n\n\n`tree` blocks\n-------------\n\n>>> n = NexusReader(os.path.join(EXAMPLE_DIR, 'example.trees'))\n>>> n.trees.ntrees\n3\n>>> n.trees.trees[0][0:60]\n'tree tree.0.1065.603220 = (((((((Chris:0.0668822155,Bruce:0.'\n\n>>> for tree in n.trees: #doctest: +SKIP\n\n\n\nWriting a Nexus File\n--------------------\n>>> from nexus import NexusWriter\n>>> n = NexusWriter()\n\nAdd a comment to appear in the header of the 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