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'})
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'
})
__maintainer__ = "Rob Knight"
__email__ = "*****@*****.**"
__status__ = "Production"
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.
__version__ = "1.5.3"
__maintainer__ = "Rob Knight"
__email__ = "*****@*****.**"
__status__ = "Development"
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))
accnum_wrapper = FieldWrapper(['Accession','Gi','Strain','Start','End'], pipes)
def _read_accnum(line):
"""Reads ACCNUM lines: format is Accession|Gi|Strain|Start|End."""
return MappedRecord(accnum_wrapper(line))
map_wrapper = FieldWrapper(['Location','Source','Type'], pipes)
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)