#!/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, parse and parse_primers"""
import os as _os
import re as _re
import io as _io
import textwrap as _textwrap
from Bio import SeqIO as _SeqIO
from pydna.genbankfile import GenbankFile as _GenbankFile
from pydna.dseqrecord import Dseqrecord as _Dseqrecord
from pydna.primer import Primer as _Primer
[docs]def parse(data, ds=True):
"""Return *all* DNA sequences found in data.
If no sequences are found, an empty list is returned. This is a greedy
function, use carefully.
Parameters
----------
data : string or iterable
The data parameter is a string containing:
1. an absolute path to a local file.
The file will be read in text
mode and parsed for EMBL, FASTA
and Genbank sequences. Can be
a string or a Path object.
2. a string containing one or more
sequences in EMBL, GENBANK,
or FASTA format. Mixed formats
are allowed.
3. data can be a list or other iterable where the elements are 1 or 2
ds : bool
If True double stranded :class:`Dseqrecord` objects are returned.
If False single stranded :class:`Bio.SeqRecord` [#]_ objects are
returned.
Returns
-------
list
contains Dseqrecord or SeqRecord objects
References
----------
.. [#] http://biopython.org/wiki/SeqRecord
See Also
--------
read
"""
def embl_gb_fasta(raw, ds, path=None):
# regex = r"^>.+?^(?=$|LOCUS|ID|>|\#)|^(?:LOCUS|ID).+?^//"
regex = (r"(?:>.+\n^(?:^[^>]+?)(?=\n\n|>|"
r"LOCUS|ID))|(?:(?:LOCUS|ID)(?:(?:.|\n)+?)^//)")
result_list = []
rawseqs = _re.findall(regex, _textwrap.dedent(raw + "\n\n"),
flags=_re.MULTILINE)
for rawseq in rawseqs:
handle = _io.StringIO(rawseq)
circular = False
try:
parsed = _SeqIO.read(handle, "embl")
except ValueError:
handle.seek(0)
try:
parsed = _SeqIO.read(handle, "genbank")
if "circular" in str(parsed.annotations.get("topology")).lower():
circular = True
except ValueError:
handle.seek(0)
try:
parsed = _SeqIO.read(handle, "fasta")
except ValueError:
parsed = ""
handle.close()
if "circular" in rawseq.splitlines()[0].lower().split():
# hack to pick up topology from malformed files
circular = True
if parsed:
from copy import deepcopy as _deepcopy # TODO: clean up !
from pydna.seqfeature import SeqFeature as _SeqFeature
nfs = [_SeqFeature() for f in parsed.features]
for f, nf in zip(parsed.features, nfs):
nf.__dict__ = _deepcopy(f.__dict__)
parsed.features = nfs
if ds and path:
result_list.append(
_GenbankFile.from_SeqRecord(
parsed, linear=not circular,
circular=circular,
path=path
)
)
elif ds:
result_list.append(
_Dseqrecord.from_SeqRecord(
parsed, linear=not circular, circular=circular
)
)
else:
parsed.annotations.update({"molecule_type": "DNA"})
result_list.append(parsed)
return result_list
# a string is an iterable datatype but on Python2.x
# it doesn't have an __iter__ method.
if not hasattr(data, "__iter__") or isinstance(data, (str, bytes)):
data = (data,)
sequences = []
for item in data:
try:
# item is a path to a utf-8 encoded text file?
with open(item, "r", encoding="utf-8") as f:
raw = f.read()
except IOError:
# item was not a path, add sequences parsed from item
raw = item
path = None
else:
# item was a readable text file, seqences are parsed from the file
path = item
finally:
sequences.extend(embl_gb_fasta(raw, ds, path))
return sequences
[docs]def parse_primers(data):
""" """
return [_Primer(x) for x in parse(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