def test_Seq__split_id_line(line, exp_id, exp_desc):
""" Are we splitting the fasta header lines correctly? """
act_id, act_desc = Seq._split_id_line(line)
assert act_id == exp_id
assert act_desc == exp_desc
return
def test_Seq_parse(fasta, expected):
actual = Seq.parse(fasta)
# We want parse to return a generator over the sequences.
assert isinstance(actual, GeneratorType)
# Just this time, get a list so we can compare lenths.
actual = list(actual)
assert len(actual) == len(expected)
for act, exp in zip(actual, expected):
assert act.id == exp.id
assert act.desc == exp.desc
assert act.seq == exp.seq
return
def main():
""" The command line version of pcalign.
This is the entrypoint specified in setup.py as `pcalign`.
"""
args = cli(prog=sys.argv[0], args=sys.argv[1:])
if args.verbose > 1:
log_level = logging.DEBUG
elif args.verbose > 0:
log_level = logging.INFO
else:
log_level = logging.WARNING
logger.setLevel(log_level)
logger.info("Running pcalign")
logger.info("Using parameters:")
logger.info("- seq1 = %s", args.seq1.name)
logger.info("- seq2 = %s", args.seq2.name)
logger.info("- output = %s", args.output.name)
logger.info("- match score = %d", args.match_score)
logger.info("- mismatch score = %d", args.mismatch_score)
logger.info("- indel_score = %d", args.indel_score)
logger.info("Parsing sequences")
try:
# Use this seq1_loaded thing to see which file fails, if one does.
seq1_loaded = False
# next() will return the next element of an iterator.
# I'm using it to pop off the first sequence.
# If there were more sequences, we simply ignore them
seq1 = Seq.read(args.seq1)
seq1_loaded = True
seq2 = Seq.read(args.seq2)
except ValueError as e:
# next will yield this exception if the iterator is empty.
# This will happen if there are no fasta headers in the file.
# To handle this user error, we log the problem and stop the program.
# It's common to handle errors like this when we're dealing with user
# input.
if seq1_loaded:
fname = args.seq2.name
else:
fname = args.seq1.name
logger.error("Parsing fasta files failed.")
logger.error("Offending file is '%s'", fname)
logger.error(e)
sys.exit(1)
logger.info("Aligning sequences")
aligned = align(seq1,
seq2,
match_reward=args.match_score,
mismatch_penalty=args.mismatch_score,
indel_penalty=args.indel_score)
logger.info("Writing alignments")
for seq in aligned:
print(seq, file=args.output)
return
def test_Seq_read(fasta, expected):
actual = Seq.read(fasta)
assert actual.id == expected.id
assert actual.desc == expected.desc
assert actual.seq == expected.seq
return
def test_Seq_getitem():
""" Simple wrapper function, so gets a simple test. """
seq = Seq(id="test", desc=None, seq="aaabbbbbaaa")
assert seq[3:].seq == "bbbbbaaa"
assert seq[1].seq == "a"
return
def test_Seq_len():
""" Simple wrapper function, so gets a simple test. """
seq = Seq(id="test", desc=None, seq="four")
assert len(seq) == 4
return
TATCGATTAAGGTGCGTTTCAAGCGTTGACATTAAAGCCGAAACGCAAGGGCAATGCAAG
TTCTGGTGTAATCATGGAAGTTAATGTTGCTCGCGTGTGTCAATGCTGGGTACAGGAGAA
TAGTGTGTATGCGTGTCAGATCCCCCAGCCGCAAAGTCCCCTTCAGTCGTGCCAAGGCGG
GAAATTCCAACTCTCGTGTCCCCATTCCCGCGCCTTGCTAAAGACATTACTAGATACGCT
TGCTTACGGAGCTACGAAACATGTGTGGCAACTCTCCAGTGCGCAGCGCCCCATAGGTTA
GGCACGGAGACAGTTCGCGTACCAGGTTCTAAATTGAGTAGGTTCGCCATGAGCAGTTAC
CACATACTACCTTGTCTGACACAGGTGACATACCGGCGGGCTGAGTATTGTGATCATGGT
GCGTATATATTGTTTCCCGTCCGTCCCCCCGGTGCACGAACTATCATCTAGCCGGCTATT
TCGTTCAGTTAGCGTAGCTCGTTGCAGAGAAGTGAATTACGTTAAGGGGATGAGCGCCCA
GTCCTCGCCCTCGCCGCTGCCATGGATATAGCAACGTT""",
""">seq3
ATCCAGCT"""
]
expected = [
Seq(id="seq1", desc="testing", seq="TTTCCGGGGCACATAATCTTCAGCCGGGCGC"),
Seq(id="seq2",
desc="testing2",
seq=("ACTAAGTAGTCTTTTTGAGGTCGTTAACTCTTATAAAGCGGCGCAGCATACCTCCCGAGA"
"CTATAGTTTTTCTCAATGCTGAACGCCTCATGGCTTGCCGGGCTCAATGCTGTAATCTGT"
"CTCGGTTCCTGTATACTAGCCGGTACTCCCCAGTTAATTCGACTCGTTGTTTCTCTGTAT"
"GTCTCCGATACATCCTAATATAATGTCCCCATGCTTACGCCTATAAAATCGCAATACTGT"
"CTAAGGGAGGTCACTTAATTGTGAAGAGAGCCTAGACAGCGTTCGATTTAGAGCGTCCGT"
"ACCAGGATCTTCTATCGGGCTCTGTGATGATTATAGCTATCGCTGACCGCCGGCTCGTCC"
"TAGCGTTTAATACGGCGTACCGACCACTAGGGGGGAGGAAGTAGTTACCATTATCATCCA"
"TATCGATTAAGGTGCGTTTCAAGCGTTGACATTAAAGCCGAAACGCAAGGGCAATGCAAG"
"TTCTGGTGTAATCATGGAAGTTAATGTTGCTCGCGTGTGTCAATGCTGGGTACAGGAGAA"
"TAGTGTGTATGCGTGTCAGATCCCCCAGCCGCAAAGTCCCCTTCAGTCGTGCCAAGGCGG"
"GAAATTCCAACTCTCGTGTCCCCATTCCCGCGCCTTGCTAAAGACATTACTAGATACGCT"
"TGCTTACGGAGCTACGAAACATGTGTGGCAACTCTCCAGTGCGCAGCGCCCCATAGGTTA"
"GGCACGGAGACAGTTCGCGTACCAGGTTCTAAATTGAGTAGGTTCGCCATGAGCAGTTAC"
(6, 6): [(5, 5)],
(7, 7): [(6, 6)]
}, [("G-ATTACA", "GCATG-CU"), ("G-ATTACA", "GCA-TGCU"),
("G-ATTACA", "GCAT-GCU")]),
])
def test_backtrack(seq1, seq2, movements, expected):
alignments = backtrack(movements, seq1, seq2)
assert len(alignments) == len(expected)
for alignment in alignments:
assert alignment in expected
return
@pytest.mark.parametrize("seq1,seq2,expected", [(
Seq(id="one", desc=None, seq="GATTACA"),
Seq(id="two", desc="desc", seq="GCATGCU"),
[
Seq(id="a_0|one", desc=None, seq="G-ATTACA"),
Seq(id="a_0|two", desc="desc", seq="GCATG-CU"),
Seq(id="a_1|one", desc=None, seq="G-ATTACA"),
Seq(id="a_1|two", desc="desc", seq="GCA-TGCU"),
Seq(id="a_2|one", desc=None, seq="G-ATTACA"),
Seq(id="a_2|two", desc="desc", seq="GCAT-GCU")
],
)])
def test_align(seq1, seq2, expected):
actual = align(seq1,
seq2,
match_reward=1,
mismatch_penalty=-1,