def test_full_LOC(self):
"""LOC should behave as expected when initialized with rich data"""
data = [
"abc\t def",
" 3 \t n",
" abc \txyz\n\n",
"x\t5",
"fgh ",
"x\t3 ",
]
class rec(MappedRecord):
Required = {"abc": []}
maps = {"abc": list_adder, "x": int_setter, "fgh": bool_setter}
label_splitter = DelimitedSplitter("\t")
constructor = rec
strict = True
loc_bad = LineOrientedConstructor(data, label_splitter, maps,
constructor, strict)
self.assertRaises(FieldError, loc_bad)
strict = False
loc_good = LineOrientedConstructor(data, label_splitter, maps,
constructor, strict)
result = loc_good()
assert isinstance(result, rec)
self.assertEqual(result, {
"abc": ["def", "xyz"],
"3": "n",
"fgh": False,
"x": 3
})
def test_splitter(self):
"""StrictFieldWrapper with splitter should use that splitter"""
fields = ["label", "count"]
splitter = DelimitedSplitter(":", -1)
f = StrictFieldWrapper(fields, splitter)
self.assertEqual(f("n:k:n:a:sd "), {"label": "n:k:n:a", "count": "sd"})
self.assertEqual(f("nknasd:"), {"label": "nknasd", "count": ""})
self.assertRaises(FieldError, f, "")
def test_parsers(self):
"""DelimitedSplitter should return function with correct behavior"""
empty = DelimitedSplitter()
space = DelimitedSplitter(None)
semicolon = DelimitedSplitter(";")
twosplits = DelimitedSplitter(";", 2)
allsplits = DelimitedSplitter(";", None)
lastone = DelimitedSplitter(";", -1)
lasttwo = DelimitedSplitter(";", -2)
self.assertEqual(empty("a b c"), ["a", "b c"])
self.assertEqual(empty("abc"), ["abc"])
self.assertEqual(empty(" "), [])
self.assertEqual(empty("a b c"), space("a b c"))
self.assertEqual(semicolon(" a ; b ; c d"), ["a", "b ; c d"])
self.assertEqual(twosplits(" a ; b ; c d"), ["a", "b", "c d"])
self.assertEqual(allsplits(" a ; b ; c;;d;e ;"),
["a", "b", "c", "", "d", "e", ""])
self.assertEqual(lastone(" a ; b ; c;;d;e ;"),
["a ; b ; c;;d;e", ""])
self.assertEqual(lasttwo(" a ; b ; c;;d;e ;"),
["a ; b ; c;;d", "e", ""])
self.assertEqual(lasttwo(""), [])
self.assertEqual(lasttwo("x"), ["x"])
self.assertEqual(lasttwo("x;"), ["x", ""])
def DefaultDelimitedSplitter(delimiter):
"""Wraps delimited splitter to handle empty records"""
parser = DelimitedSplitter(delimiter=delimiter)
def f(line):
parsed = parser(line)
if len(parsed) == 1:
parsed.append("")
return parsed
return f
__email__ = "*****@*****.**"
__status__ = "Development"
maketrans = str.maketrans
strip = str.strip
rstrip = str.rstrip
def ll_start(line):
"""Returns True if line looks like the start of a LocusLink record."""
return line.startswith(">>")
LLFinder = LabeledRecordFinder(ll_start)
pipes = DelimitedSplitter("|", None)
first_pipe = DelimitedSplitter("|")
commas = DelimitedSplitter(",", None)
first_colon = DelimitedSplitter(":", 1)
accession_wrapper = FieldWrapper(["Accession", "Gi", "Strain"], pipes)
def _read_accession(line):
"""Reads accession lines: format is Accession | Gi | Strain."""
return MappedRecord(accession_wrapper(line))
rell_wrapper = FieldWrapper(["Description", "Id", "IdType", "Printable"], pipes)
result[key] = [val]
labels.append(key)
return result, labels
def is_clustal_seq_line(line):
"""Returns True if line starts with a non-blank character but not 'CLUSTAL'.
Useful for filtering other lines out of the file.
"""
return (line and (not line[0].isspace())
and (not line.startswith("CLUSTAL"))
and (not line.startswith("MUSCLE")))
last_space = DelimitedSplitter(None, -1)
def delete_trailing_number(line):
"""Deletes trailing number from a line.
WARNING: does not preserve internal whitespace when a number is removed!
(converts each whitespace run to a single space). Returns the original
line if it didn't end in a number.
"""
pieces = line.split()
try:
int(pieces[-1])
return " ".join(pieces[:-1])
except ValueError: # no trailing numbers
return line