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 test_fasta__from_lines__empty_record_name_only__first():
list(FASTA.from_lines([">fasta1\n", ">fasta2\n", "AGTC\n"]))
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_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_name__with_others():
lines = [">\n", "ACGT\n", ">Foo\n", "ACGGTA\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__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__first():
list(FASTA.from_lines([">fasta1\n", ">fasta2\n", "AGTC\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__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"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__empty_name__alone():
lines = [">\n", "ACGT\n"]
list(FASTA.from_lines(lines))
def test_fasta__from_lines__empty_name__alone():
lines = [">\n", "ACGT\n"]
list(FASTA.from_lines(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_equal(FASTA.from_lines([]), [])
def test_fasta__from_lines__no_records():
assert_list_equal(FASTA.from_lines([]), [])
