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#!/usr/bin/env python3
from Bio import SeqIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
import bz2
import gzip
import lzma
from pathlib import Path
import pytest
import random
from augur.errors import AugurError
import augur.io.sequences
def random_seq(k):
"""Generate a single random sequence of nucleotides of length k.
"""
return "".join(random.choices(("A","T","G","C"), k=k))
def generate_sequences(n, k=10):
"""Generate n random sequences of length k.
"""
return (
SeqRecord(Seq(random_seq(k)), id=f"SEQ_{i}")
for i in range(1, n + 1)
)
@pytest.fixture
def sequences():
return list(generate_sequences(3))
@pytest.fixture
def sequences_generator():
return generate_sequences(3)
@pytest.fixture
def fasta_filename(tmpdir, sequences):
filename = str(tmpdir / "sequences.fasta")
SeqIO.write(sequences, filename, "fasta")
return filename
@pytest.fixture
def additional_fasta_filename(tmpdir, sequences):
filename = str(tmpdir / "additional_sequences.fasta")
SeqIO.write(sequences, filename, "fasta")
return filename
@pytest.fixture
def gzip_fasta_filename(tmpdir, sequences):
filename = str(tmpdir / "sequences.fasta.gz")
with gzip.open(filename, "wt") as oh:
SeqIO.write(sequences, oh, "fasta")
return filename
@pytest.fixture
def bzip2_fasta_filename(tmpdir, sequences):
filename = str(tmpdir / "sequences.fasta.bz2")
with bz2.open(filename, "wt") as oh:
SeqIO.write(sequences, oh, "fasta")
return filename
@pytest.fixture
def lzma_fasta_filename(tmpdir, sequences):
filename = str(tmpdir / "sequences.fasta.xz")
with lzma.open(filename, "wt") as oh:
SeqIO.write(sequences, oh, "fasta")
return filename
@pytest.fixture
def genbank_reference():
return "tests/data/zika_outgroup.gb"
class TestReadSequences:
def test_read_sequences_from_single_file(self, fasta_filename):
sequences = augur.io.sequences.read_sequences(fasta_filename, format="fasta")
assert len(list(sequences)) == 3
def test_read_sequences_from_multiple_files(self, fasta_filename, additional_fasta_filename):
sequences = augur.io.sequences.read_sequences(fasta_filename, additional_fasta_filename, format="fasta")
assert len(list(sequences)) == 6
def test_read_sequences_from_multiple_files_or_buffers(self, fasta_filename, additional_fasta_filename):
with open(fasta_filename) as fasta_handle:
sequences = augur.io.sequences.read_sequences(fasta_handle, additional_fasta_filename, format="fasta")
assert len(list(sequences)) == 6
def test_read_single_fasta_record(self, fasta_filename):
record = next(augur.io.sequences.read_sequences(fasta_filename, format="fasta"))
assert record.id == "SEQ_1"
def test_read_single_genbank_record(self, genbank_reference):
reference = next(augur.io.sequences.read_sequences(genbank_reference, format="genbank"))
assert reference.id == "KX369547.1"
def test_read_single_genbank_record_from_a_path(self, genbank_reference):
reference = next(augur.io.sequences.read_sequences(Path(genbank_reference), format="genbank"))
assert reference.id == "KX369547.1"
def test_read_sequences_from_single_gzip_file(self, gzip_fasta_filename):
sequences = augur.io.sequences.read_sequences(gzip_fasta_filename, format="fasta")
assert len(list(sequences)) == 3
def test_read_sequences_from_single_lzma_file(self, lzma_fasta_filename):
sequences = augur.io.sequences.read_sequences(lzma_fasta_filename, format="fasta")
assert len(list(sequences)) == 3
def test_read_sequences_from_single_bzip2_file(self, bzip2_fasta_filename):
sequences = augur.io.sequences.read_sequences(bzip2_fasta_filename, format="fasta")
assert len(list(sequences)) == 3
def test_read_sequences_from_multiple_files_with_different_compression(self, fasta_filename, gzip_fasta_filename, lzma_fasta_filename):
sequences = augur.io.sequences.read_sequences(fasta_filename, gzip_fasta_filename, lzma_fasta_filename, format="fasta")
assert len(list(sequences)) == 9
class TestWriteSequences:
def test_write_sequences(self, tmpdir, sequences):
output_filename = Path(tmpdir) / Path("new_sequences.fasta")
sequences_written = augur.io.sequences.write_sequences(sequences, output_filename, "fasta")
assert sequences_written == len(sequences)
def test_write_genbank_sequence(self, tmpdir, genbank_reference):
output_filename = Path(tmpdir) / Path("new_sequences.fasta")
reference = SeqIO.read(genbank_reference, "genbank")
sequences_written = augur.io.sequences.write_sequences([reference], output_filename, "genbank")
assert sequences_written == 1
def test_write_sequences_from_generator(self, tmpdir, sequences_generator):
output_filename = Path(tmpdir) / Path("new_sequences.fasta")
sequences_written = augur.io.sequences.write_sequences(sequences_generator, output_filename, "fasta")
assert sequences_written == 3
def test_write_single_set_of_sequences_to_gzip_file(self, tmpdir, sequences):
output_filename = Path(tmpdir) / Path("new_sequences.fasta.gz")
sequences_written = augur.io.sequences.write_sequences(sequences, output_filename, "fasta")
assert sequences_written == len(sequences)
with gzip.open(output_filename, "rt") as handle:
assert sequences_written == len([line for line in handle if line.startswith(">")])
def test_write_single_set_of_sequences_to_bzip2_file(self, tmpdir, sequences):
output_filename = Path(tmpdir) / Path("new_sequences.fasta.bz2")
sequences_written = augur.io.sequences.write_sequences(sequences, output_filename, "fasta")
assert sequences_written == len(sequences)
with bz2.open(output_filename, "rt") as handle:
assert sequences_written == len([line for line in handle if line.startswith(">")])
def test_write_single_set_of_sequences_to_lzma_file(self, tmpdir, sequences):
output_filename = Path(tmpdir) / Path("new_sequences.fasta.xz")
sequences_written = augur.io.sequences.write_sequences(sequences, output_filename, "fasta")
assert sequences_written == len(sequences)
with lzma.open(output_filename, "rt") as handle:
assert sequences_written == len([line for line in handle if line.startswith(">")])
def test_write_sequences_by_external_handle(self, tmpdir, sequences):
output_filename = Path(tmpdir) / Path("new_sequences.fasta")
with open(output_filename, "w") as handle:
total_sequences_written = 0
for sequence in sequences:
sequences_written = augur.io.sequences.write_sequences(
sequence,
handle
)
total_sequences_written += sequences_written
with open(output_filename, "r") as handle:
assert total_sequences_written == len([line for line in handle if line.startswith(">")])
@pytest.fixture()
def sequence_records():
return [
{"strain": "SEQ_A", "sequence": "AAAA"},
{"strain": "SEQ_T", "sequence": "TTTT"},
{"strain": "SEQ_C", "sequence": "CCCC"},
{"strain": "SEQ_G", "sequence": "GGGG"},
]
class TestWriteFastaFromRecords:
def test_write_records_to_fasta(self, tmpdir, sequence_records):
output_fasta = str(tmpdir / "sequences.fasta")
records = list(augur.io.sequences.write_records_to_fasta(sequence_records, output_fasta))
assert all("sequence" not in record for record in records)
with open(output_fasta, 'r') as handle:
assert len(records) == len([line for line in handle if line.startswith(">")])
def test_write_records_to_fasta_with_bad_id_field(self, tmpdir, sequence_records):
output_fasta = str(tmpdir / "sequences.fasta")
seq_id_field = "bogus_id"
with pytest.raises(AugurError) as e_info:
list(augur.io.sequences.write_records_to_fasta(sequence_records, output_fasta, seq_id_field=seq_id_field))
assert str(e_info.value) == f"Provided sequence identifier field {seq_id_field!r} does not exist."
def test_write_records_to_fasta_with_bad_seq_field(self, tmpdir, sequence_records):
output_fasta = str(tmpdir / "sequences.fasta")
seq_field = "bogus_sequence"
with pytest.raises(AugurError) as e_info:
list(augur.io.sequences.write_records_to_fasta(sequence_records, output_fasta, seq_field=seq_field))
assert str(e_info.value) == f"Provided sequence field {seq_field!r} does not exist."
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