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#!/usr/bin/env python
# Copyright 2005 Gavin E. Crooks <gec@threeplusone.com>
# Copyright 2005-2006 The Regents of the University of California.
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
"""Read the sequence data from a nexus file.
This IO code only gives read access to the sequence data.
Reference:
'NEXUS: An extensible file format for systematic information'
Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621
"""
from typing import Iterator, Optional, TextIO
from ..seq import Alphabet, Seq, SeqList
from ._nexus import Nexus, safename
names = ("nexus", "paup")
extensions = ("nex", "nexus", "paup", "nxs")
def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]:
"""Iterate over the sequences in the file."""
# Default implementation
return iter(read(fin, alphabet))
def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList:
"""Extract sequence data from a nexus file."""
n = Nexus(fin)
seqs = []
for taxon in n.taxlabels:
name = safename(taxon)
r = n.matrix[taxon]
if alphabet is None:
s = Seq(r, name=name, alphabet=r.alphabet)
else:
s = Seq(r, name=name, alphabet=alphabet)
seqs.append(s)
if len(seqs) == 0:
# Something went terrible wrong.
raise ValueError("Cannot parse file")
return SeqList(seqs)
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