def test_perfect_match():
s = "aaacttcccaccccataccctattaccactgccaattacctagtggtttcatttactctaaacctgtgattcctctgaattattttcatttta"
r1 = SeqRecord(seq=Seq(s), annotations={"topology": "linear"})
r2 = SeqRecord(seq=Seq(s), annotations={"topology": "linear"})
blaster = BioBlast([r1], [r2])
blaster.blastn()
result = blaster.results[0]
assert result["query"]["start"] == 1
assert result["query"]["end"] == len(s)
assert result["subject"]["start"] == 1
assert result["subject"]["end"] == len(s)
def test_simple_alignment():
record = rand_record(1000)
queries = [record[:]]
subjects = [record[10:-10]]
queries = make_linear(queries)
subjects = make_linear(subjects)
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
assert len(results) == 1
compare_result(results[0], 11, len(record) - 10, 1, len(record) - 10 - 10)
def test_circular_over_subject(self):
record = rand_record(1000)
queries = [record]
subjects = [record[200:300] + ns(500) + record[100:200]]
queries = make_linear(queries)
subjects = make_circular(subjects)
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
compare_result(results[0], 101, 300, 601, 100)
def test_align_Ns():
record = rand_record(1000)
nseq = SeqRecord(Seq("N" * 500))
queries = [record[:]]
subjects = [nseq + record + nseq]
queries = make_linear(queries)
subjects = make_linear(subjects)
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
print(results)
def test_self_blast(here):
subjects = load_genbank_glob(join(here,
"data/test_data/genbank/templates/*.gb"),
force_unique_ids=True)
queries = [
SeqRecord(Seq(str(subjects[0][:1000].seq))),
# SeqRecord(Seq(str(subjects[1][:1000]))),
]
force_unique_record_ids(make_linear(queries))
bioblast = BioBlast(queries, queries)
results = bioblast.blastn()
assert not results
def test_run_bioblast_twice():
junk1 = "atgctatgctgatgctgctgtgctgatgctgatgtgtattgctgtatcgcgcgagttagc"
junk2 = "g" * 30
frag = "aaacttcccaccccataccctattaccactgccaattacctagtggtttcatttactctaaacctgtgattcctctgaattattttcatttta"
query = SeqRecord(seq=Seq(frag), annotations={"circular": False})
subject = SeqRecord(seq=Seq(junk1 + frag + junk2),
annotations={"circular": False})
blaster = BioBlast([subject], [query])
blaster.blastn()
blaster.blastn()
alignments = blaster.results
print(alignments)
def test_partial_alignment(left_spacer, ij):
record = rand_record(1000)
queries = [record[:]]
subjects = [ns(left_spacer) + record[ij[0]:ij[1]]]
queries = make_linear(queries)
subjects = make_linear(subjects)
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
assert len(results) == 1
compare_result(results[0], ij[0] + 1, ij[1], 1 + left_spacer,
ij[1] - ij[0] + left_spacer)
def test_partial_alignment_reverse_complement(left_spacer, ij):
record = rand_record(1000)
queries = [record[:]]
subjects = [record[ij[0]:ij[1]]]
subjects[0] = ns(left_spacer) + subjects[0].reverse_complement()
queries = make_linear(queries)
subjects = make_linear(subjects)
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
assert len(results) == 1
compare_result(results[0], ij[0] + 1, ij[1], len(subjects[0].seq),
left_spacer + 1)
def test_circular_complete_subject(self):
record = rand_record(1000)
queries = [record]
subjects = [record[500:] + record[:400]]
queries = make_circular(queries)
subjects = make_linear(subjects)
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
result = results[0]
print(result)
assert result["subject"]["start"] == 1
assert result["subject"]["end"] == 900
assert result["query"]["start"] == 501
assert result["query"]["end"] == 400
def test_raises_pyblast_when_not_unique(here):
subjects = load_genbank_glob(
join(here, "data/test_data/genbank/templates/*.gb"))
queries = load_genbank_glob(
join(here, "data/test_data/genbank/designs/*.gb"))
print("n_queres: {}".format(len(queries)))
print("n_subjects: {}".format(len(subjects)))
with pytest.raises(PyBlastException):
BioBlast(subjects, queries)
def test_reverse_alignment_simple():
record = rand_record(1000)
query = record
subject = record[10:990].reverse_complement()
subjects = make_linear([subject])
queries = make_linear([query])
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
for k, v in bioblast.seq_db.records.items():
print(k)
print(v)
print(json.dumps(results, indent=2))
assert results[0]["query"]["start"] == 10 + 1
assert results[0]["query"]["end"] == 990
assert results[0]["subject"]["start"] == 980
assert results[0]["subject"]["end"] == 1
def test_not_raise_pyblast_when_unique(here):
subjects = load_genbank_glob(
join(here, "data/test_data/genbank/templates/*.gb"))
queries = load_genbank_glob(
join(here, "data/test_data/genbank/designs/*.gb"))
force_unique_record_ids(subjects + queries)
print("n_queres: {}".format(len(queries)))
BioBlast(subjects, queries)
def test_multiquery_blast(here):
subjects = load_genbank_glob(join(here,
"data/test_data/genbank/templates/*.gb"),
force_unique_ids=True)
queries = load_genbank_glob(join(here,
"data/test_data/genbank/designs/*.gb"),
force_unique_ids=True)
print("n_queres: {}".format(len(queries)))
print("n_subjects: {}".format(len(subjects)))
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
recids = set()
for res in results:
recid = res["query"]["origin_record_id"]
recids.add(recid)
print("n_records: {}".format(len(results)))
assert len(recids) == len(queries)
def test_circular_complete_query_1(self):
"""In this situation, the subject is completely aligned with a circular query
starting at index 500 (starting index = 0). Note that the
pyblast results start at index 1."""
record = rand_record(1000)
queries = [record]
subjects = [ns(100) + record[500:] + record[:500] + ns(100)]
queries = make_circular(queries)
subjects = make_linear(subjects)
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
result = results[0]
assert result["query"]["start"] == 501
assert result["query"]["raw_end"] == 1500
assert result["subject"]["start"] == 101
assert result["subject"]["end"] == 1100
def test_circular_over_query(self):
record = rand_record(1000)
queries = [record]
subjects = [record[-100:] + record[:100]]
queries = make_circular(queries)
subjects = make_linear(subjects)
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
result = results[0]
result_seq = str((record[result["query"]["start"] - 1:] +
record[:result["query"]["end"]]).seq)
expected_seq = str(subjects[0].seq)
assert result_seq == expected_seq
compare_result(results[0], 1000 - 100 + 1, 100, 1, 200)
def test_example2():
from pyblast import BioBlast
from pyblast.utils import make_linear, make_circular
from Bio.SeqRecord import SeqRecord
from Bio.Seq import Seq
import json
seq = "ACGTTGTAGTGTAGTTGATGATGATGTCTGTGTCGTGTGATGTGCTAGGGGTTGATGTGAGTAGTTAGTGGTAGTGTTTAGGGGCGGCGCGGAGTATGCTG"
queries = [SeqRecord(Seq(seq))]
subjects = [SeqRecord(Seq(seq[-20:] + seq[:30]))]
# pyblast requires a 'topology' annotation on the SeqRecords.
# we can make records circular or linear using `make_linear` or `make_circular` methods
subjects = make_linear(subjects)
queries = make_circular(queries)
blast = BioBlast(subjects, queries)
results = blast.blastn()
print(json.dumps(results, indent=2))
def test_basic_run_reverse_complement():
junk1 = "atgctatgctgatgctgctgtgctgatgctgatgtgtattgctgtatcgcgcgagttagc"
junk2 = "g" * 30
frag = "aaacttcccaccccataccctattaccactgccaattacctagtggtttcatttactctaaacctgtgattcctctgaattattttcatttta"
query = SeqRecord(seq=Seq(frag), annotations={
"circular": False
}).reverse_complement()
subject = SeqRecord(seq=Seq(junk1 + frag + junk2),
annotations={"circular": False})
make_linear([query])
# print(type(query))
# print(type(subject))
blaster = BioBlast([subject], [query])
blaster.blastn()
alignments = blaster.results
for a in alignments:
print(json.dumps(a, indent=2))
assert a["subject"]["strand"] == -1
def test_circular_complete_query_4(self):
"""In this situation, the subject is wraps around the query for 10
extra bases on the left and right site.
Note that pyblast results start at index 1.
"""
record = rand_record(1000)
queries = [record]
subjects = [ns(100) + record[-10 + 500:] + record[:500 + 10] + ns(100)]
queries = make_circular(queries)
subjects = make_linear(subjects)
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
result = results[0]
assert result["query"]["start"] == 491
assert result["query"]["raw_end"] == 1510
assert result["subject"]["start"] == 101
assert result["subject"]["end"] == 1120
def test_interaction_network():
"""We expect self alignments to be removed from the results."""
records = [None, None, None, None]
records[0] = rand_record(500)
records[1] = rand_record(100) + records[0][:-100] + rand_record(1000)
records[2] = rand_record(200) + records[1][:700] + rand_record(500)
records[3] = records[2][-500:] + rand_record(500)
force_unique_record_ids(records)
queries = make_linear(records)
bioblast = BioBlast(queries, queries)
results = bioblast.blastn()
assert results
for r in results:
k1 = r["query"]["origin_key"]
k2 = r["subject"]["origin_key"]
print(k1, k2)
assert not k1 == k2
def test_circular_complete_query_parametrized_rc(self, extra_right,
extra_left):
record = rand_record(1000)
queries = [record]
subjects = [
ns(100) + record[(500 - extra_left):] +
record[:(500 + extra_right)] + ns(100)
]
subjects = [subjects[0].reverse_complement()]
queries = make_circular(queries)
subjects = make_linear(subjects)
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
result = results[0]
print(json.dumps(result, indent=2))
assert result["query"]["start"] == 501 - extra_left
assert result["query"]["raw_end"] == 1500 + extra_right
assert result["subject"]["start"] == 1100 + extra_right + extra_left
assert result["subject"]["end"] == 101
# to spans
query_span = bioblast.parse_result_to_span(result["query"],
output_index=0)
subject_span = bioblast.parse_result_to_span(result["subject"],
output_index=0)
assert len(subject_span) == len(
query_span) == 1000 + extra_right + extra_left
assert query_span.a == 500 - extra_left
assert query_span.b == 500 + extra_right
assert subject_span.a == 100
assert subject_span.b == 1100 + extra_right + extra_left
def test_unnamed_queries(here):
subjects = load_genbank_glob(join(here,
"data/test_data/genbank/templates/*.gb"),
force_unique_ids=True)
seqstr1 = str(subjects[0].seq)[:1000]
seqstr2 = str(subjects[1].seq)[:1000]
queries = [
SeqRecord(Seq(seqstr1)),
SeqRecord(Seq(seqstr2))
# SeqRecord(Seq(str(subjects[1][:1000]))),
]
force_unique_record_ids(make_linear(queries))
bioblast = BioBlast(subjects, queries)
results = bioblast.blastn()
recids = set()
for res in results:
recid = res["query"]["origin_record_id"]
recids.add(recid)
print("n_records: {}".format(len(results)))
assert len(recids) == len(queries)
def make_blast():
subjects = load_fasta_glob(join(
here, "data/test_data/primers/primers.fasta"),
force_unique_ids=True)
subjects = make_linear(subjects)
queries = load_genbank_glob(
join(
here,
"data/test_data/genbank/designs/pmodkan-ho-pact1-z4-er-vpr.gb"
),
force_unique_ids=True,
)
return BioBlast(subjects, queries)
def make_blast():
subjects = load_genbank_glob(join(
here, "data/test_data/genbank/templates/*.gb"),
force_unique_ids=True)
queries = load_genbank_glob(
join(
here,
"data/test_data/genbank/designs/pmodkan-ho-pact1-z4-er-vpr.gb"
),
force_unique_ids=True,
)
queries = make_circular(queries)
assert is_circular(queries[0])
return BioBlast(subjects, queries)
def test_unnamed_queries_raises_duplicate_error(here):
subjects = load_genbank_glob(join(here,
"data/test_data/genbank/templates/*.gb"),
force_unique_ids=True)
seqstr1 = str(subjects[0].seq)[:1000]
seqstr2 = str(subjects[1].seq)[:1000]
queries = [
SeqRecord(Seq(seqstr1)),
SeqRecord(Seq(seqstr2))
# SeqRecord(Seq(str(subjects[1][:1000]))),
]
make_linear(queries)
with pytest.raises(PyBlastException):
BioBlast(subjects, queries)
def test_ungapped():
frag = "GtctaaaggtgaagaattattcactggtgttgtcccaattttggttgaattagatggtgatgttaatggtcacaaattttctgtctccggtgaaggtgaaggtgatgctacttacggtaaattgaccttaaaatttatttgtactactggtaaattgccagttccatggccaaccttagtcactactttcggttatggtgttcaatgttttgcgagatacccagatcatatgaaacaacatgactttttcaagtctgccatgccagaaggttatgttcaagaaagaactatttttttcaaagatgacggtaactacaagaccagagctgaagtcaagtttgaaggtgataccttagttaatagaatcgaattaaaaggtattgattttaaagaagatggtaacattttaggtcacaaattggaatacaactataactctcacaatgtttacatcatggctgacaaacaaaagaatggtatcaaagttaacttcaaaattagacacaacattgaagatggttctgttcaattagctgaccattatcaacaaaatactccaattggtgatggtccagtcttgttaccagacaaccattacttatccactcaatctgccttatccaaagatccaaacgaaaagagagaccacatggtcttgttagaatttgttactgctgctggtattacccatggtatggatgaattgtacaaaTAGTGATACCGTCGACCTCGAGTCAattagttatgtcacgcttacattcacgccctccccccacatccgctctaaccgaaaaggaaggagttagacaacctgaagtctaggtccctatttatttttttatagttatgttagtattaagaacgttatttatatttcaaatttttcttt"
query = SeqRecord(seq=Seq(frag), annotations={"circular": False})
subject = SeqRecord(
seq=Seq(frag[:400] + "atgctatgctgatgctgctgtgctgat" + frag[400:]),
annotations={"circular": False},
)
# print(type(query))
# print(type(subject))
blaster = BioBlast([subject], [query])
blaster.update_config({"ungapped": None})
blaster.blastn()
alignments = blaster.results
print(alignments)
))
]
subjects = [
SeqRecord(Seq("TCGTGTAGTTGAGTGTTACGTTGCATGTCGTTACGTGATCG"), id="aa1"),
SeqRecord(Seq("TCGTGTAGTTGAGTGTTACGTTGCATGTCGGGGACGTGATCG"), id="aa2")
]
# pyblast requires a 'topology' annotation on the SeqRecords.
# we can make records circular or linear using `make_linear` or `make_circular` methods
t0 = time.time()
subjects = make_linear(subjects)
queries = make_linear(queries)
blast = BioBlast(subjects, queries)
results = blast.blastn()
t1 = time.time() - t0
#print(t1)
#print(results)
fa_file = "../samples/P21333.fasta"
sequences = SeqIO.parse(fa_file, "fasta")
queries = []
subjects = []
for record in sequences:
queries.append(record)
#sequences = SeqIO.parse("viral/viral_classification/sample_genomes/HIV.B.fasta", "fasta")
sequences = SeqIO.parse("../samples/H1.txt", "fasta")
