def test_splitter(self):
"""FieldWrapper with splitter should use that splitter"""
fields = ["label", "count"]
splitter = DelimitedSplitter(":", -1)
f = FieldWrapper(fields, splitter)
self.assertEqual(f(""), {})
self.assertEqual(f("nknasd:"), {"label": "nknasd", "count": ""})
self.assertEqual(f("n:k:n:a:sd "), {"label": "n:k:n:a", "count": "sd"})
def test_default(self):
"""Default FieldWrapper should wrap fields and labels"""
fields = list("abcde")
f = FieldWrapper(fields)
self.assertEqual(f(""), {})
self.assertEqual(f("xy za "), {"a": "xy", "b": "za"})
self.assertEqual(
f("1 2\t\t 3 \n4 5 6"),
{"a": "1", "b": "2", "c": "3", "d": "4", "e": "5"},
)
maketrans = str.maketrans
strip = str.strip
rstrip = str.rstrip
all_chars = maketrans("", "")
dna_lc = "utacgrywsmkbdhvn"
dna_lc_cmp = "aatgcyrwskmvhdbn"
dna_trans = maketrans(dna_lc + dna_lc.upper(), dna_lc_cmp + dna_lc_cmp.upper())
rna_lc = "utacgrywsmkbdhvn"
rna_lc_cmp = "aaugcyrwskmvhdbn"
rna_trans = maketrans(rna_lc + rna_lc.upper(), rna_lc_cmp + rna_lc_cmp.upper())
locus_fields = [
None, "locus", "length", None, "mol_type", "topology", "db", "date"
]
_locus_parser = FieldWrapper(locus_fields)
# need to turn off line stripping, because whitespace is significant
GbFinder = DelimitedRecordFinder("//", constructor=rstrip)
class PartialRecordError(Exception):
pass
def parse_locus(line):
"""Parses a locus line, including conversion of Length to an int.
WARNING: Gives incorrect results on legacy records that omit the topology.
All records spot-checked on 8/30/05 had been updated to include the topology
even when prior versions omitted it.
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)
def _read_rell(line):
"""Reads RELL lines: format is Description|Id|IdType|Printable"""
return MappedRecord(rell_wrapper(line))
def test_constructor(self):
"""FieldWrapper with constructor should use that constructor"""
fields = list("abc")
f = FieldWrapper(fields, constructor=fake_dict)
self.assertEqual(f("x y"), {"a": "x", "b": "y"})
assert isinstance(f("x y"), fake_dict)
