def test_remove_non_word_characters(self):
header = EMBLHeader()
test_cases = [
('foo', 'foo'),
('#foo', 'foo'),
('#fo!o', 'foo'),
('fo#o', 'foo'),
('foo##', 'foo'),
("*!#foo", 'foo')
]
for test_string, expected_result in test_cases:
self.assertEqual(header.remove_non_word_characters(test_string), expected_result)
def test_build_source_attributes(self):
header = EMBLHeader()
calculated_attributes=header.build_source_attributes(organism="an organism", taxon_id="TAX_ID", sequence_name="sequence_name")
expected_attributes = {"organism": "an organism", "db_xref": "taxon:TAX_ID", "note": "sequence_name"}
self.assertEqual(calculated_attributes, expected_attributes)
def test_format_long_publication(self):
header = EMBLHeader()
header.authors="Jagger M., Richards K., Watts C., Wood R., Jones B., Stewart I., Wyman B., Taylor M."
header.classification="UNC"
header.genome_type="circular"
header.organism="organism"
header.project="PRJ1234"
header.publication="The Rolling Stones, 12 X 5, The Rolling Stones No. 2, Out of Our Heads, Aftermath, Between the Buttons, Their Satanic Majesties Request, Beggars Banquet"
header.sequence_identifier="contig123"
header.sequence_length=1234
header.sequence_name="chromX"
header.taxon_id=5678
header.title="Let It Bleed, Sticky Fingers, Exile on Main St., Goats Head Soup, It's Only Rock 'n Roll, Black and Blue, Some Girls, Emotional Rescue, Tattoo You, Undercover"
source_attributes = {"organism": header.organism, "db_xref": "taxon:5678", "note": "chromX"}
header.source_feature = EMBLFeature('source', 1, 1234, '+', source_attributes)
expected_header = """\
ID XXX; XXX; circular; genomic DNA; STD; UNC; 1234 BP.
XX
AC XXX;
XX
AC * _contig123
XX
PR Project:PRJ1234;
XX
DE XXX;
XX
RN [1]
RA Jagger M., Richards K., Watts C., Wood R., Jones B., Stewart I., Wyman B.,
RA Taylor M.;
RT "Let It Bleed, Sticky Fingers, Exile on Main St., Goats Head Soup, It's
RT Only Rock 'n Roll, Black and Blue, Some Girls, Emotional Rescue, Tattoo
RT You, Undercover";
RL The Rolling Stones, 12 X 5, The Rolling Stones No. 2, Out of Our Heads,
RL Aftermath, Between the Buttons, Their Satanic Majesties Request, Beggars
RL Banquet.
XX
FH Key Location/Qualifiers
FH
FT source 1..1234
FT /organism="organism"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:5678"
FT /note="chromX"
"""
calculated_header = header.format()
for calculated_line,expected_line in zip(calculated_header.split('\n'), expected_header.split('\n')):
self.assertEqual(calculated_line, expected_line)
self.assertEqual(len(calculated_header), len(expected_header))
def test_format_long_organism_name(self):
header = EMBLHeader()
header.authors="John Doe"
header.classification="UNC"
header.genome_type="circular"
header.organism="reeeeeeeeeeeeeeaaaaaaaaaaaaaallllllllllyyyyyyyyyyyyyyyyyyyy_long_name"
header.project="PRJ1234"
header.publication="Unpublished"
header.sequence_identifier="contig123"
header.sequence_length=1234
header.sequence_name="chromX"
header.taxon_id=5678
header.title="My title"
source_attributes = {"organism": header.organism, "db_xref": "taxon:5678", "note": "chromX"}
header.source_feature = EMBLFeature('source', 1, 1234, '+', source_attributes)
expected_header = """\
ID XXX; XXX; circular; genomic DNA; STD; UNC; 1234 BP.
XX
AC XXX;
XX
AC * _contig123
XX
PR Project:PRJ1234;
XX
DE XXX;
XX
RN [1]
RA John Doe;
RT "My title";
RL Unpublished.
XX
FH Key Location/Qualifiers
FH
FT source 1..1234
FT /organism="reeeeeeeeeeeeeeaaaaaaaaaaaaaallllllllllyyyyyyyy
FT yyyyyyyyyyyy_long_name"
FT /mol_type="genomic DNA"
FT /db_xref="taxon:5678"
FT /note="chromX"
"""
calculated_header = header.format()
for calculated_line,expected_line in zip(calculated_header.split('\n'), expected_header.split('\n')):
self.assertEqual(calculated_line, expected_line)
self.assertEqual(len(calculated_header), len(expected_header))