"""Module contains objects for importing and exporting parts and sequences."""
from basicsynbio.decorators import addargs2docs
from basicsynbio.main import CommonArgDocs, IP_SEQREC, IS_SEQREC, seqrec2part
import basicsynbio as bsb
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
import io
import json
import os
import tempfile
from typing import Union, Iterable, Iterator, Generator
from sbol2 import Document
[docs]@addargs2docs(
CommonArgDocs.HANDLE,
CommonArgDocs.FORMAT,
CommonArgDocs.ADD_I_SEQS,
CommonArgDocs.BASIC_PART,
)
def import_part(handle: str, format: str, add_i_seqs: bool = False) -> bsb.BasicPart:
"""Imports a Part object using Bio.SeqIO.read().
Note:
Refer to Biopython documentation for further information on Bio.SeqIO.read().
Args:
handle:
format:
add_i_seqs:
Returns:
BasicPart:
"""
seqrec = SeqIO.read(handle, format)
return seqrec2part(seqrec, add_i_seqs)
[docs]@addargs2docs(CommonArgDocs.ADD_I_SEQS, CommonArgDocs.BASIC_PARTS)
def import_sbol_parts(
path: str, add_i_seqs=False
) -> Generator[bsb.BasicPart, None, None]:
"""Imports BasicPart objects using sbol2.Document.exportToFormat.
Note:
Refer to Biopython documentation for further information on Bio.SeqIO.read().
Refer to pysbol2 documentation for further information.
Args:
path: path to SBOL file.
add_i_seqs:
Yields:
BasicPart:
"""
doc = Document(path)
fp = tempfile.NamedTemporaryFile(delete=False)
doc.exportToFormat("GenBank", fp.name)
seqrecs = SeqIO.parse(fp.name, "genbank")
fp.close()
os.unlink(fp.name)
yield from (seqrec2part(seqrec, add_i_seqs) for seqrec in seqrecs)
[docs]@addargs2docs(
CommonArgDocs.HANDLE,
CommonArgDocs.FORMAT,
CommonArgDocs.ADD_I_SEQS,
CommonArgDocs.BASIC_PARTS,
)
def import_parts(handle: str, format: str, add_i_seqs=False) -> Iterable[bsb.BasicPart]:
"""Imports a Generator of BasicPart objects using Bio.SeqIO.parse().
Note:
Refer to Biopython documentation for further information on Bio.SeqIO.parse().
Args:
handle:
format:
add_i_seqs:
Yields:
BasicPart:
"""
seqrecs = SeqIO.parse(handle, format)
yield from (seqrec2part(seqrec, add_i_seqs) for seqrec in seqrecs)
[docs]@addargs2docs(CommonArgDocs.HANDLE, CommonArgDocs.FORMAT)
def export_sequences_to_file(
sequences: Iterable[Union[SeqRecord, bsb.BasicPart, bsb.BasicAssembly]],
handle: str,
format: str = "genbank",
molecule_type: str = "DNA",
) -> None:
"""Exports sequences to file using Bio.SeqIO.write().
Note:
Refer to Biopython documentation for further information on Bio.SeqIO.write().
Args:
sequences: Sequences to export.
handle:
format:
molecule_type (optional): Type of molecule within sequences.
defaults to 'DNA'.
Raises:
ValueError: sequences was not of correct type.
"""
if type(sequences) in [bsb.BasicPart, bsb.BasicAssembly, SeqRecord]:
SeqIO.write(_process_basic_object(sequences, molecule_type), handle, format)
elif hasattr(sequences, "__iter__"):
sequences = (
_process_basic_object(basic_object, molecule_type)
for basic_object in sequences
)
SeqIO.write(sequences, handle, format)
else:
raise TypeError(
"sequences was not iterable or of type BasicPart, BasicAssembly or SeqRecord"
)
def _process_basic_object(basic_object, molecule_type):
"""Converts basic_object into an object that can be processed by Bio.SeqIO."""
try:
basic_object = basic_object.return_seqrec()
except AttributeError:
pass
basic_object.annotations["molecule_type"] = molecule_type
return basic_object