def test_parse_fasta__multiple_records():
lines = [">first\n", "TGTTCTCCACCGTGCACAAC\n", "CCTTCATCCA\n",
">Second XT:1:0\n", "GAGAGCTCAGCTAAC\n",
">Third\n", "CGCTGACCAAAAACGGACAG\n", "GGCATTCGGC\n"]
expected = [(("first", None), "TGTTCTCCACCGTGCACAACCCTTCATCCA"),
(("Second", "XT:1:0"), "GAGAGCTCAGCTAAC"),
(("Third", None), "CGCTGACCAAAAACGGACAGGGCATTCGGC")]
assert_list_equals(parse_fasta(lines), expected)
def test_parse_fasta__multiple_records():
lines = [
">first\n", "TGTTCTCCACCGTGCACAAC\n", "CCTTCATCCA\n",
">Second XT:1:0\n", "GAGAGCTCAGCTAAC\n", ">Third\n",
"CGCTGACCAAAAACGGACAG\n", "GGCATTCGGC\n"
]
expected = [(("first", None), "TGTTCTCCACCGTGCACAACCCTTCATCCA"),
(("Second", "XT:1:0"), "GAGAGCTCAGCTAAC"),
(("Third", None), "CGCTGACCAAAAACGGACAGGGCATTCGGC")]
assert_list_equals(parse_fasta(lines), expected)
def parse_msa(lines, read_meta = False):
"""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."""
msa, metas = {}, {}
for ((name, meta), sequence) in parse_fasta(lines):
if name in msa:
raise MSAError("Duplicate names found, cannot be represented as MSA: " + name)
msa[name] = sequence
metas[name] = meta
validate_msa(msa)
if read_meta:
return msa, metas
return msa
def parse_msa(lines, read_meta=False):
"""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."""
msa, metas = {}, {}
for ((name, meta), sequence) in parse_fasta(lines):
if name in msa:
raise MSAError(
"Duplicate names found, cannot be represented as MSA: " + name)
msa[name] = sequence
metas[name] = meta
validate_msa(msa)
if read_meta:
return msa, metas
return msa
def test_parse_fasta__single_record():
lines = [">single\n", "TGTTCTCCACCGTGCACAAC\n", "CCTTCATCCA\n"]
expected = [(("single", None), "TGTTCTCCACCGTGCACAACCCTTCATCCA")]
assert_list_equals(parse_fasta(lines), expected)
def test_parse_fasta__no_records():
assert_list_equals(parse_fasta([]), [])
def test_parse_fasta__empty_name__alone():
lines = [">\n", "ACGT\n"]
list(parse_fasta(lines))
def test_parse_fasta__missing_name__alone():
lines = ["ACGT\n"]
list(parse_fasta(lines))
def test_parse_fasta__empty_record__middle():
lines = [">fasta0\n", "ACGT\n", ">fasta1\n", ">fasta2\n", "AGTC\n"]
list(parse_fasta(lines))
def test_parse_empty_record_last():
lines = [">fasta1\n", "ACGT\n", ">fasta2\n"]
list(parse_fasta(lines))
def test_parse_fasta__empty_record__middle():
lines = [">fasta0\n", "ACGT\n", ">fasta1\n", ">fasta2\n", "AGTC\n"]
list(parse_fasta(lines))
def test_parse_fasta__empty_record_name_only__first():
list(parse_fasta([">fasta1\n", ">fasta2\n", "AGTC\n"]))
def test_parse_fasta__empty_record_name_only__nothing_else():
list(parse_fasta([">fasta1\n"]))
def test_parse_fasta__single_record():
lines = [">single\n", "TGTTCTCCACCGTGCACAAC\n", "CCTTCATCCA\n"]
expected = [(("single", None), "TGTTCTCCACCGTGCACAACCCTTCATCCA")]
assert_list_equals(parse_fasta(lines), expected)
def test_parse_fasta__no_records():
assert_list_equals(parse_fasta([]), [])
def test_parse_fasta__empty_record_name_only__nothing_else():
list(parse_fasta([">fasta1\n"]))
def test_parse_fasta__empty_record_name_only__first():
list(parse_fasta([">fasta1\n", ">fasta2\n", "AGTC\n"]))
def test_parse_fasta__missing_name__alone():
lines = ["ACGT\n"]
list(parse_fasta(lines))
def test_parse_empty_record_last():
lines = [">fasta1\n", "ACGT\n", ">fasta2\n"]
list(parse_fasta(lines))
def test_parse_fasta__missing_name__with_others():
lines = ["ACGT\n", ">Foo\n", "ACGGTA\n"]
list(parse_fasta(lines))
def test_parse_fasta__missing_name__with_others():
lines = ["ACGT\n", ">Foo\n", "ACGGTA\n"]
list(parse_fasta(lines))
def test_parse_fasta__empty_name__alone():
lines = [">\n", "ACGT\n"]
list(parse_fasta(lines))
def test_parse_fasta__empty_name__with_others():
lines = [">\n", "ACGT\n", ">Foo\n", "ACGGTA\n"]
list(parse_fasta(lines))
def test_parse_fasta__empty_name__with_others():
lines = [">\n", "ACGT\n", ">Foo\n", "ACGGTA\n"]
list(parse_fasta(lines))