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f2004e04da37fdf4aaa3b0aa437363421b31629e
biopython/Tests/test_SeqIO_SnapGene.py
Manuel Lera-Ramirez f2004e04da added test and docstring for #5053
2025-10-01 19:19:11 +01:00

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# Copyright 2019 Damien Goutte-Gattat. All rights reserved.
#
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Tests for the SeqIO SnapGene module."""
import datetime
import unittest
from io import BytesIO
from Bio import SeqIO
from Bio.SeqFeature import CompoundLocation
class TestSnapGene(unittest.TestCase):
sample_data = {
"sample-d": {
"file": "SnapGene/sample-d.dna",
"name": "Sample",
"id": "Sample",
"description": "Sample Sequence D",
"length": 1000,
"topology": "linear",
"date": datetime.datetime(2021, 7, 7, 0, 0),
"features": [
{
"type": "misc_binding",
"start": 499,
"end": 700,
"strand": 1,
"label": ["FeatureB"],
"note": ["Sample feature B"],
},
{
"type": "promoter",
"start": 49,
"end": 150,
"strand": 1,
"label": ["FeatureA"],
"note": ["Sample feature A"],
},
{
"type": "misc_feature",
"start": 700,
"end": 720,
"strand": 1,
"label": ["FeatureC"],
"note": [
"Sample feature C, with explicit label",
"Another note for sample feature C",
],
},
{
"type": "misc_feature",
"start": 720,
"end": 740,
"strand": 1,
"label": ["SampleFeatureD"],
"note": [
"Sample feature D, with a label different from the feature name"
],
"name": "FeatureD",
},
],
},
"sample-e": {
"file": "SnapGene/sample-e.dna",
"name": "Sample",
"id": "Sample",
"description": "Sample Sequence E",
"length": 1000,
"date": datetime.datetime(2019, 8, 3, 0, 0),
"topology": "circular",
"features": [
{
"type": "terminator",
"start": 399,
"end": 750,
"strand": -1,
"label": ["FeatureB"],
},
{
"type": "rep_origin",
"start": 160,
"end": 241,
"strand": 1,
"label": ["FeatureA"],
},
],
},
"sample-f": {
"file": "SnapGene/sample-f.dna",
"name": "Sample",
"id": "Sample",
"description": "Sample Sequence F",
"length": 1000,
"date": datetime.datetime(2023, 1, 22, 0, 0),
"topology": "circular",
"features": [
{
"type": "terminator",
"start": 399,
"end": 724,
"strand": -1,
"label": ["FeatureB"],
"note": ["An example of a reverse-strand split feature"],
"parts": ["1:subfeature1;3:subfeature3"],
"segments": [
{"start": 634, "end": 724},
{"start": 516, "end": 634},
{"start": 399, "end": 499},
],
},
{
"type": "rep_origin",
"start": 160,
"end": 241,
"strand": 1,
"label": ["FeatureA"],
"note": ["An example of a split feature"],
"parts": ["2:subfeature2"],
"segments": [
{"start": 160, "end": 180},
{"start": 187, "end": 207},
{"start": 214, "end": 241},
],
},
{
"type": "primer_bind",
"start": 751,
"end": 776,
"strand": 1,
"label": ["Primer 1"],
},
],
},
"pFA-KanMX4": {
"file": "SnapGene/pFA-KanMX4.dna",
"name": "<unknown name>",
"id": "<unknown id>",
"description": "<unknown description>",
"length": 3941,
"date": datetime.datetime(2020, 7, 30, 0, 0),
"topology": "circular",
"features": [
{
"type": "promoter",
"start": 0,
"end": 3941,
"strand": 1,
"label": ["SP6 promoter"],
},
{
"type": "promoter",
"start": 1578,
"end": 1597,
"strand": -1,
"label": ["T7 promoter"],
},
{
"type": "promoter",
"start": 3474,
"end": 3579,
"strand": -1,
"label": ["AmpR promoter"],
},
{
"type": "terminator",
"start": 1273,
"end": 1471,
"strand": 1,
"label": ["TEF terminator"],
},
{
"type": "promoter",
"start": 114,
"end": 458,
"strand": 1,
"label": ["TEF promoter"],
},
{
"type": "rep_origin",
"start": 1854,
"end": 2443,
"strand": -1,
"label": ["ori"],
},
{
"type": "CDS",
"start": 458,
"end": 1268,
"strand": 1,
"label": ["KanR"],
},
{
"type": "CDS",
"start": 2613,
"end": 3474,
"strand": -1,
"label": ["AmpR"],
"parts": ["1:signal sequence"],
"segments": [
{"start": 3405, "end": 3474},
{"start": 2613, "end": 3405},
],
},
{
"type": "gene",
"start": 114,
"end": 1471,
"strand": 1,
"label": ["kanMX"],
},
],
},
}
def _check_multivalued_qualifier(self, qualifier, expected, actual):
if qualifier in expected:
for value in expected[qualifier]:
self.assertIn(value, actual.qualifiers[qualifier])
def _check_feature_segments(self, segments, feature):
self.assertIsInstance(feature.location, CompoundLocation)
self.assertEqual(len(segments), len(feature.location.parts))
for i in range(len(segments)):
segment = segments[i]
location = feature.location.parts[i]
self.assertEqual(segment["start"], location.start)
self.assertEqual(segment["end"], location.end)
def test_read(self):
"""Read sample files."""
for sample in self.sample_data.values():
record = SeqIO.read(sample["file"], "snapgene")
self.assertEqual(sample["name"], record.name)
self.assertEqual(sample["id"], record.id)
self.assertEqual(sample["description"], record.description)
self.assertEqual(sample["length"], len(record))
self.assertEqual(sample["date"], record.annotations["date"])
self.assertEqual(sample["topology"], record.annotations["topology"])
self.assertEqual(len(sample["features"]), len(record.features))
for i in range(len(sample["features"])):
exp_feat = sample["features"][i]
read_feat = record.features[i]
self.assertEqual(exp_feat["type"], read_feat.type)
self.assertEqual(exp_feat["start"], read_feat.location.start)
self.assertEqual(exp_feat["end"], read_feat.location.end)
self.assertEqual(exp_feat["strand"], read_feat.location.strand)
self._check_multivalued_qualifier("label", exp_feat, read_feat)
self._check_multivalued_qualifier("note", exp_feat, read_feat)
self._check_multivalued_qualifier("parts", exp_feat, read_feat)
if "name" in exp_feat:
self.assertEqual(exp_feat["name"], read_feat.qualifiers["name"][0])
else:
self.assertTrue("name" not in read_feat.qualifiers)
if "segments" in exp_feat:
self._check_feature_segments(exp_feat["segments"], read_feat)
def test_filter_with_hybridization_params(self):
"""Ensure only releveant `primer_bind` features from SnapGene files are retained in
the `SeqRecord`. See the docstring of `_parse_primers_packet` for more details.
"""
record = SeqIO.read("SnapGene/sample-hybridization-params.dna", "snapgene")
count_primer_features = 0
for feature in record.features:
if "XhoI-hht2(US)-Fwd" in feature.qualifiers["label"]:
count_primer_features += 1
self.assertEqual(count_primer_features, 1)
class TestCorruptedSnapGene(unittest.TestCase):
def setUp(self):
with open("SnapGene/sample-d.dna", "rb") as f:
self.buffer = f.read()
def munge_buffer(self, position, value):
mod_buffer = bytearray(self.buffer)
if isinstance(value, list):
mod_buffer[position : position + len(value) - 1] = value
else:
mod_buffer[position] = value
return BytesIO(mod_buffer)
def test_invalid_cookie(self):
"""Read a file with missing or invalid cookie packet."""
# Remove the first packet
h = BytesIO(self.buffer[19:])
with self.assertRaisesRegex(
ValueError, "The file does not start with a SnapGene cookie packet"
):
SeqIO.read(h, "snapgene")
h.close()
# Keep the first packet but destroy the magic cookie
h = self.munge_buffer(5, [0x4B, 0x41, 0x42, 0x4F, 0x4F, 0x4D])
with self.assertRaisesRegex(
ValueError, "The file is not a valid SnapGene file"
):
SeqIO.read(h, "snapgene")
h.close()
def test_missing_dna(self):
"""Read a file without a DNA packet."""
# Simulate a missing DNA packet by changing the tag byte to an
# unknown packet type, so that the parser will skip the packet.
h = self.munge_buffer(19, 0x80)
with self.assertRaisesRegex(ValueError, "No DNA packet in file"):
SeqIO.read(h, "snapgene")
h.close()
def test_extra_dna(self):
"""Read a file with supernumerary DNA packet."""
# Fabricate a file with a duplicated DNA packet
buf = bytearray(self.buffer)
buf.extend(self.buffer[19:1025]) # Append duplicated DNA packet
h = BytesIO(buf)
with self.assertRaisesRegex(
ValueError, "The file contains more than one DNA packet"
):
SeqIO.read(h, "snapgene")
h.close()
def test_truncated_packet(self):
"""Read a file with incomplete packet."""
# Truncate before the end of the length bytes
h = BytesIO(self.buffer[3:])
with self.assertRaisesRegex(ValueError, "Unexpected end of packet"):
SeqIO.read(h, "snapgene")
h.close()
# Truncate before the end of the data
h = BytesIO(self.buffer[10:])
with self.assertRaisesRegex(ValueError, "Unexpected end of packet"):
SeqIO.read(h, "snapgene")
h.close()
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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