def from_lines(cls, lines):
"""Parses a MSA from a file/list of lines, and returns a dictionary
of names to sequences. If read_meta is True, meta information included
after the first space in header of each sequence:
>NAME META-INFORMATION
SEQUENCE
As suggested above, sequences are expected to be in FASTA format."""
return MSA(FASTA.from_lines(lines))
def from_lines(cls, lines):
"""Parses a MSA from a file/list of lines, and returns a dictionary
of names to sequences. If read_meta is True, meta information included
after the first space in header of each sequence:
>NAME META-INFORMATION
SEQUENCE
As suggested above, sequences are expected to be in FASTA format."""
return MSA(FASTA.from_lines(lines))
def test_fasta__from_lines__multiple_records():
lines = [">first\n", "TGTTCTCCACCGTGCACAAC\n", "CCTTCATCCA\n",
">Second XT:1:0\n", "GAGAGCTCAGCTAAC\n",
">Third\n", "CGCTGACCAAAAACGGACAG\n", "GGCATTCGGC\n"]
expected = [FASTA("first", None, "TGTTCTCCACCGTGCACAACCCTTCATCCA"),
FASTA("Second", "XT:1:0", "GAGAGCTCAGCTAAC"),
FASTA("Third", None, "CGCTGACCAAAAACGGACAGGGCATTCGGC")]
assert_list_equal(FASTA.from_lines(lines), expected)
def test_fasta__from_lines__multiple_records():
lines = [">first\n", "TGTTCTCCACCGTGCACAAC\n", "CCTTCATCCA\n",
">Second XT:1:0\n", "GAGAGCTCAGCTAAC\n",
">Third\n", "CGCTGACCAAAAACGGACAG\n", "GGCATTCGGC\n"]
expected = [FASTA("first", None, "TGTTCTCCACCGTGCACAACCCTTCATCCA"),
FASTA("Second", "XT:1:0", "GAGAGCTCAGCTAAC"),
FASTA("Third", None, "CGCTGACCAAAAACGGACAGGGCATTCGGC")]
assert_list_equal(FASTA.from_lines(lines), expected)
def _read_mitochondria(self, tar_handle, filename):
try:
tar_handle.getmember(filename)
except KeyError:
# Missing MT file is allowed
return None
handle = tar_handle.extractfile(filename)
results = {}
for record in FASTA.from_lines(handle):
record = FASTA(name=record.name,
meta=record.meta,
sequence=record.sequence.upper())
unexpected = set(record.sequence) - set("ACGTN-")
if unexpected:
unexpected = ", ".join(map(repr, sorted(unexpected)))
raise ZonkeyDBError("Unexpected nucleotide in %s; only A, C, "
"G, T, N, and - are allowed, not %s"
% (unexpected, filename))
elif record.name in results:
raise ZonkeyDBError("Duplicate sequence name in %s: %r"
% (filename, record.name))
results[record.name] = record
lengths = frozenset(len(record.sequence)
for record in results.itervalues())
if not lengths:
raise ZonkeyDBError("No mitochondrial sequences found in %r"
% (filename,))
elif len(lengths) > 2:
lengths = tuple(sorted(lengths))
lengths_s = "%s, and %s" % (", ".join(map(str, lengths[:-1])),
lengths[-1])
raise ZonkeyDBError("At most two different sequence lengths "
"expected for mitochondrial sequences, but "
"found %i different lengths in %r: %s"
% (len(lengths), filename, lengths_s))
elif len(lengths) != 1:
# Unpadded sequences are allowed
delta_len = max(lengths) - min(lengths)
mito_padding = self.settings["MitoPadding"]
if (delta_len != mito_padding):
raise ZonkeyDBError("Length difference between mitochondrial "
"sequences in %r does not match the "
"padding; expected a difference of %i bp, "
"but found a %i bp difference."
% (filename, mito_padding, delta_len))
return results
def _read_mitochondria(self, tar_handle, filename):
try:
tar_handle.getmember(filename)
except KeyError:
# Missing MT file is allowed
return None
handle = tar_handle.extractfile(filename)
results = {}
for record in FASTA.from_lines(handle):
record = FASTA(name=record.name,
meta=record.meta,
sequence=record.sequence.upper())
unexpected = set(record.sequence) - set("ACGTN-")
if unexpected:
unexpected = ", ".join(map(repr, sorted(unexpected)))
raise ZonkeyDBError("Unexpected nucleotide in %s; only A, C, "
"G, T, N, and - are allowed, not %s" %
(unexpected, filename))
elif record.name in results:
raise ZonkeyDBError("Duplicate sequence name in %s: %r" %
(filename, record.name))
results[record.name] = record
lengths = frozenset(
len(record.sequence) for record in results.itervalues())
if not lengths:
raise ZonkeyDBError("No mitochondrial sequences found in %r" %
(filename, ))
elif len(lengths) > 2:
lengths = tuple(sorted(lengths))
lengths_s = "%s, and %s" % (", ".join(map(
str, lengths[:-1])), lengths[-1])
raise ZonkeyDBError("At most two different sequence lengths "
"expected for mitochondrial sequences, but "
"found %i different lengths in %r: %s" %
(len(lengths), filename, lengths_s))
elif len(lengths) != 1:
# Unpadded sequences are allowed
delta_len = max(lengths) - min(lengths)
mito_padding = self.settings["MitoPadding"]
if (delta_len != mito_padding):
raise ZonkeyDBError("Length difference between mitochondrial "
"sequences in %r does not match the "
"padding; expected a difference of %i bp, "
"but found a %i bp difference." %
(filename, mito_padding, delta_len))
return results
def test_fasta__from_lines_single_record():
lines = [">single\n", "TGTTCTCCACCGTGCACAAC\n", "CCTTCATCCA\n"]
expected = [FASTA("single", None, "TGTTCTCCACCGTGCACAACCCTTCATCCA")]
assert list(FASTA.from_lines(lines)) == list(expected)
def test_fasta__from_lines__empty_name__alone():
lines = [">\n", "ACGT\n"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__empty_record_last():
lines = [">fasta1\n", "ACGT\n", ">fasta2\n"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__empty_record_name_only__first():
list(FASTA.from_lines([">fasta1\n", ">fasta2\n", "AGTC\n"]))
def test_fasta__from_lines__no_records():
assert_list_equal(FASTA.from_lines([]), [])
def test_fasta__from_lines__empty_name__with_others():
lines = [">\n", "ACGT\n", ">Foo\n", "ACGGTA\n"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__no_records():
assert list(FASTA.from_lines([])) == list([])
def test_fasta__from_lines__empty_name__alone():
lines = [">\n", "ACGT\n"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__missing_name__alone():
lines = ["ACGT\n"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__empty_record_last():
lines = [">fasta1\n", "ACGT\n", ">fasta2\n"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__empty_record__middle():
lines = [">fasta0\n", "ACGT\n", ">fasta1\n", ">fasta2\n", "AGTC\n"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__empty_record_name_only__nothing_else():
list(FASTA.from_lines([">fasta1\n"]))
def test_fasta__from_lines_single_record():
lines = [">single\n", "TGTTCTCCACCGTGCACAAC\n", "CCTTCATCCA\n"]
expected = [FASTA("single", None, "TGTTCTCCACCGTGCACAACCCTTCATCCA")]
assert_list_equal(FASTA.from_lines(lines), expected)
def test_fasta__from_lines__empty_record_name_only__nothing_else():
with pytest.raises(FASTAError):
list(FASTA.from_lines([">fasta1\n"]))
def test_fasta__from_lines__empty_record_name_only__nothing_else():
list(FASTA.from_lines([">fasta1\n"]))
def test_fasta__from_lines__empty_record_name_only__first():
with pytest.raises(FASTAError):
list(FASTA.from_lines([">fasta1\n", ">fasta2\n", "AGTC\n"]))
def test_fasta__from_lines__empty_record__middle():
lines = [">fasta0\n", "ACGT\n", ">fasta1\n", ">fasta2\n", "AGTC\n"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__empty_record_last():
lines = [">fasta1\n", "ACGT\n", ">fasta2\n"]
with pytest.raises(FASTAError):
list(FASTA.from_lines(lines))
def test_fasta__from_lines__missing_name__alone():
lines = ["ACGT\n"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__missing_name__alone():
with pytest.raises(FASTAError):
list(FASTA.from_lines(["ACGT\n"]))
def test_fasta__from_lines__empty_name__with_others():
lines = [">\n", "ACGT\n", ">Foo\n", "ACGGTA\n"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__empty_name__alone():
with pytest.raises(FASTAError):
list(FASTA.from_lines([">\n", "ACGT\n"]))
def test_fasta__from_lines__empty_name__with_others():
with pytest.raises(FASTAError):
list(FASTA.from_lines([">\n", "ACGT\n", ">Foo\n", "ACGGTA\n"]))
def test_fasta__from_lines__no_records():
assert_list_equal(FASTA.from_lines([]), [])
