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"""
Tests for `bx.seq.seq`.
"""
import unittest
import bx.seq
from bx.seq import (
fasta_tests,
nib_tests,
qdna_tests,
)
test_fa = "test_data/seq_tests/test.fa"
test2_fa = "test_data/seq_tests/test2.fa"
test_nib = "test_data/seq_tests/test.nib"
test_qdna = "test_data/seq_tests/test.qdna"
valid_fasta = fasta_tests.valid_seq
valid_nib = nib_tests.valid_seq
valid_qdna = qdna_tests.valid_seq
# Same sequences as stored in test2.fa
valid2_fa = [
("apple", "GGCGCTGCGATAAGGTTGCGACAACACGGACCTTCTTTTGCCTACCTCTGTTCTTGGCACG"),
("orange", "CGTGCCGAGAACAGAAAATACGCCGGGCGGTGCAGTAGTATCTTGGTATCCGATATGCAGG"),
("grapefruit", "CCTGCATATCGACTAGTACACCCTCCCGAGGTACCCCACCCATCCCTCTTTTCTCGGCGCG"),
]
class SEQTestCase(unittest.TestCase):
def test_get_fasta(self):
fastafile = bx.seq.seq_file(open(test_fa, "rb"))
check_get(fastafile, valid_fasta, 3, 40)
def test_get_nib(self):
nibfile = bx.seq.seq_file(open(test_nib, "rb"))
check_get(nibfile, valid_nib, 3, 40)
def test_get_qdna(self):
qdnafile = bx.seq.seq_file(open(test_qdna, "rb"))
check_get(qdnafile, valid_qdna, 3, 40)
def test_get_reader(self):
reader = bx.seq.seq_reader(open(test2_fa, "rb"))
for ix, seq in enumerate(reader):
assert ix < len(valid2_fa), "FastaReader returns too many sequences"
text = f"{seq}"
fields = text.split()
assert len(fields) == 2, 'SeqReader.__str__ returns incorrect sequence string "%s" (%d)' % text
assert (
fields[0] == valid2_fa[ix][0]
), f"FastaReader returned the wrong name ({fields[0]},{valid2_fa[ix][0]})"
assert (
fields[1] == valid2_fa[ix][1]
), f"FastaReader returned the wrong text ({fields[1]},{valid2_fa[ix][1]})"
def check_get(seqfile, valid_seq, start, len):
assert seqfile.get(start, len) == valid_seq[start : start + len]
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