def _read_sts(line):
"""Reads STS lines: format is in the full docstring.
Format:
Name|Chromosome|StsId|Segment|SequenceKnown|Evidence
"""
return MappedRecord(sts_wrapper(line))
def _read_sts(line):
"""Turns an STS line (without label) into a record.
Infuritatingly, STS lines are not semicolon-delimited, and spaces appear
in places they shouldn't. This was the case as of 10/9/03: expect this
'feature' to be unstable!
"""
filtered = line.replace('=', ' ')
return MappedRecord(list(ByPairs(filtered.split())))
def _read_cdd(line):
"""Reads CDD lines: format is Name|Key|Score|EValue|BitScore."""
return MappedRecord(cdd_wrapper(line))
def _read_map(line):
"""Reads MAP lines: format is Location|Source|Type."""
return MappedRecord(map_wrapper(line))
def _read_rell(line):
"""Reads RELL lines: format is Description|Id|IdType|Printable"""
return MappedRecord(rell_wrapper(line))
def _read_accnum(line):
"""Reads ACCNUM lines: format is Accession|Gi|Strain|Start|End."""
return MappedRecord(accnum_wrapper(line))
def _read_contig(line):
"""Reads CONTIG lines. Format described in full docstring.
Accession|Gi|Strain|From|To|Orientation|Chromosome|Assembly
"""
return MappedRecord(contig_wrapper(line))
def _read_accession(line):
"""Reads accession lines: format is Accession | Gi | Strain."""
return MappedRecord(accession_wrapper(line))
def _read_go(line):
"""Reads GO lines. Format: Category|Term|EvidenceCode|GoId|Source|PubMedId"""
return MappedRecord(go_wrapper(line))
def _read_extannot(line):
"""Reads EXTANNOT lines. format: Category|Term|EvidenceCode|Source|PubMedId"""
return MappedRecord(extannot_wrapper(line))
def _read_grif(line):
"""Reads GRIF lines: format is PubMedId|Description."""
return MappedRecord(grif_wrapper(line))
def _read_comp(line):
"""Reads COMP lines: format is in the full docstring.
TaxonId|Symbol|Chromosome|Position|LocusId|ChromosomeSelf|SymbolSelf|MapName
"""
return MappedRecord(comp_wrapper(line))
def test_init_data(self):
"""MappedRecord should work like normal dict init"""
exp = {'a': 3, 'b': 4}
self.assertEqual(MappedRecord({'a': 3, 'b': 4}), exp)
self.assertEqual(MappedRecord(a=3, b=4), exp)
self.assertEqual(MappedRecord([['a', 3], ['b', 4]]), exp)
def test_init_empty(self):
"""MappedRecord empty init should work OK"""
g = MappedRecord()
self.assertEqual(g, {})
def setUp(self):
"""Define a few standard MappedRecords"""
self.empty = MappedRecord()
self.single = MappedRecord({'a': 3})
self.several = MappedRecord(a=4, b=5, c='a', d=[1, 2, 3])