#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2013-2020 by Björn Johansson. All rights reserved.
# This code is part of the Python-dna distribution and governed by its
# license. Please see the LICENSE.txt file that should have been included
# as part of this package.
"""Provides two functions, read and read_primer."""
from pydna.parsers import parse as _parse
from pydna.primer import Primer as _Primer
[docs]def read(data, ds=True):
"""This function is similar the :func:`parse` function but expects one and only
one sequence or and exception is thrown.
Parameters
----------
data : string
see below
ds : bool
Double stranded or single stranded DNA, if True return
Dseqrecord objects, else Bio.SeqRecord objects.
Returns
-------
Dseqrecord
contains the first Dseqrecord or SeqRecord object parsed.
Notes
-----
The data parameter is similar to the data parameter for :func:`parse`.
See Also
--------
parse
"""
results = _parse(data, ds)
try:
results = results.pop()
except IndexError:
raise ValueError("No sequences found in data:\n({})".format(data[:79]))
return results
[docs]def read_primer(data):
"""Use this function to read a primer sequence from a string or a local file.
The usage is similar to the :func:`parse_primer` function."""
return _Primer(read(data, ds=False))
if __name__ == "__main__":
import os as _os
cached = _os.getenv("pydna_cached_funcs", "")
_os.environ["pydna_cached_funcs"] = ""
import doctest
doctest.testmod(verbose=True, optionflags=doctest.ELLIPSIS)
_os.environ["pydna_cached_funcs"] = cached