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#!/usr/bin/env python
# Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
#
# 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 and write a rectangular array of sequence data.
One sequence per line and nothing else. Each line must contain the same number
of characters. Blank lines and white space are ignored.
--- Example Array ---
--------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF
--------------------------LENLEDLF-WELDRLD------NYNDTSLVENH-
--------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY
-----------------------------------YTSDN---------YSGSGDYDSNK
-SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD
--LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD
-SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD
-EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD
"""
from typing import Generator, Optional, TextIO
from ..seq import Alphabet, Seq, SeqList
from ..utils import remove_whitespace
example = """
--------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF
--------------------------LENLEDLF-WELDRLD------NYNDTSLVENH-
--------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY
-----------------------------------YTSDN---------YSGSGDYDSNK
-SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD
--LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD
-SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD
-EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD
"""
names = ("array", "flatfile")
extensions = ()
def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList:
"""Read a file of raw sequence alignment data.
Args:
fin -- A stream or file to read
alphabet -- The expected alphabet of the data, if given
Returns:
SeqList -- A list of sequences
Raises:
ValueError -- If the file is unparsable
"""
seqs = [s for s in iterseq(fin, alphabet)]
return SeqList(seqs)
def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Generator:
"""Read one line of sequence data and yield the sequence.
Args:
fin -- A stream or file to read
alphabet -- The expected alphabet of the data, if given
Yields:
Seq -- One alphabetic sequence at a time.
Raises:
ValueError -- If the file is unparsable
"""
alphabet = Alphabet(alphabet)
line_length = 0
for linenum, line in enumerate(fin):
if line.isspace():
continue # Blank line
line = line.strip()
if line[0] == ">": # probably a fasta file. Fail.
raise ValueError("Parse Error on input line: %d " % linenum)
line = remove_whitespace(line)
if not alphabet.alphabetic(line):
raise ValueError(
"Character on line: %d not in alphabet: %s : %s"
% (linenum, alphabet, line)
)
if line_length and line_length != len(line):
raise ValueError("Line %d has an incommensurate length." % linenum)
line_length = len(line)
yield Seq(line, alphabet)
def write(afile: TextIO, seqs: SeqList) -> None:
"""Write raw sequence data, one line per sequence.
arguments:
afile -- A writable stream.
seqs -- A list of Seq's
"""
for s in seqs:
writeseq(afile, s)
def writeseq(afile: TextIO, seq: SeqList) -> None:
"""Write a single sequence in raw format.
arguments:
afile -- A writable stream.
seq -- A Seq instance
"""
print(seq, file=afile)
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