def test_fastq_itemizer(self):
'It tests the fasta itemizer'
fhand = StringIO('@s1\nACTG\n+\n1234\n@s2 desc\nACTG\n+\n4321\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['@s1\n', 'ACTG\n', '+\n', '1234\n'], {}),
('s2', ['@s2 desc\n', 'ACTG\n', '+\n', '4321\n'], {})]
# Empty line
fhand = StringIO('@s1\nACTG\n+\n1234\n\n@s2 desc\nACTG\n+\n4321\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['@s1\n', 'ACTG\n', '+\n', '1234\n'], {}),
('s2', ['@s2 desc\n', 'ACTG\n', '+\n', '4321\n'], {})]
# Empty line
fhand = StringIO('@s1\nACTG\nATTA\n+\n1234\n1234\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['@s1\n', 'ACTGATTA\n', '+\n',
'12341234\n'], {})]
def test_fastq_itemizer(self):
'It tests the fasta itemizer'
fhand = StringIO('@s1\nACTG\n+\n1234\n@s2 desc\nACTG\n+\n4321\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['@s1\n', 'ACTG\n', '+\n', '1234\n'], {}),
('s2', ['@s2 desc\n', 'ACTG\n', '+\n', '4321\n'], {})]
# Empty line
fhand = StringIO('@s1\nACTG\n+\n1234\n\n@s2 desc\nACTG\n+\n4321\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['@s1\n', 'ACTG\n', '+\n', '1234\n'], {}),
('s2', ['@s2 desc\n', 'ACTG\n', '+\n', '4321\n'], {})]
# Empty line
fhand = StringIO('@s1\nACTG\nATTA\n+\n1234\n1234\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['@s1\n', 'ACTGATTA\n', '+\n', '12341234\n'],
{})]
def test_fasta_itemizer(self):
'It tests the fasta itemizer'
fhand = StringIO('>s1\nACTG\n>s2 desc\nACTG\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['>s1\n', 'ACTG\n'], {}),
('s2', ['>s2 desc\n', 'ACTG\n'], {})]
# with several lines
fhand = StringIO('>s1\nACTG\nGTAC\n>s2 desc\nACTG\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['>s1\n', 'ACTGGTAC\n'], {}),
('s2', ['>s2 desc\n', 'ACTG\n'], {})]
# With empty lines
fhand = StringIO('>s1\nACTG\n\n>s2 desc\nACTG\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['>s1\n', 'ACTG\n'], {}),
('s2', ['>s2 desc\n', 'ACTG\n'], {})]
def test_fasta_itemizer(self):
'It tests the fasta itemizer'
fhand = StringIO('>s1\nACTG\n>s2 desc\nACTG\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['>s1\n', 'ACTG\n'], {}),
('s2', ['>s2 desc\n', 'ACTG\n'], {})]
# with several lines
fhand = StringIO('>s1\nACTG\nGTAC\n>s2 desc\nACTG\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['>s1\n', 'ACTGGTAC\n'], {}),
('s2', ['>s2 desc\n', 'ACTG\n'], {})]
# With empty lines
fhand = StringIO('>s1\nACTG\n\n>s2 desc\nACTG\n')
seqs = list(_itemize_fastx(fhand))
assert seqs == [('s1', ['>s1\n', 'ACTG\n'], {}),
('s2', ['>s2 desc\n', 'ACTG\n'], {})]
def test_singleline_itemizer(self):
fhand = StringIO('@s1\nACTG\n+\n1234\n' * 1100)
seqs = list(_itemize_fastx(fhand))
names = [seq[0] for seq in seqs]
assert len(names) == 1100
assert len(set([seq[1][1] for seq in seqs])) == 1
def test_singleline_itemizer(self):
fhand = StringIO('@s1\nACTG\n+\n1234\n' * 1100)
seqs = list(_itemize_fastx(fhand))
names = [seq[0] for seq in seqs]
assert len(names) == 1100
assert len(set([seq[1][1] for seq in seqs])) == 1