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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 sequence information in tab-delimited format.
This very simple format has two columns per line. The first column is a sequence name, the second
column is the sequence itself. The columns are separated by a single tab ("\\t") character.
"""
from typing import Iterator, List, Optional, TextIO
from ..seq import Alphabet, Seq, SeqList
names = ("table", "tab")
extensions = ("tbl",)
example = """
EC0001 MKRISTTITTTITITTGNGAG
EC0002 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAM
EC0003 MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLG
EC0004 MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLD
EC0005 MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYYWDGGH
EC0006 MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQISTLM
EC0007 MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNS
EC0008 MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRK
EC0009 MNTLRIGLVSISDRASSGVYQDKGIPALEEWLTSALTTPFELETRLIPDE
EC0010 MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQ
"""
def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList:
"""Read and parse file.
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) -> Iterator[Seq]:
"""Parse a file and generate sequences.
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)
for lineno, line in enumerate(fin):
line = line.strip()
if line == "":
continue
columns = line.split("\t")
if len(columns) != 2:
raise ValueError(
"Parse failed on line %d: did not find two columns separated by a tab."
% lineno
)
yield Seq(columns[1], alphabet=alphabet, name=columns[0])
def write(fout: TextIO, seqs: List[Seq]) -> None:
"""Write a two column, tab-delimited file.
Args:
fout -- A writable stream.
seqs -- A list of Seq's
"""
for s in seqs:
writeseq(fout, s)
def writeseq(fout: TextIO, seq: Seq) -> None:
"""Write a single sequence in fasta format.
Args:
afile -- A writable stream.
seq -- A Seq instance
"""
name = seq.name or ""
print(name, seq, sep="\t", file=fout)
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