def test_twoheaders(self):
fmt = FastqFormat()
with open_output(self.path, "w") as fw:
fw.write(fmt.format(Sequence("name", "CCATA", "!#!#!", name2="name")))
fw.write(fmt.format(Sequence("name2", "HELLO", "&&&!&", name2="name2")))
with open(self.path) as t:
assert t.read() == '@name\nCCATA\n+name\n!#!#!\n@name2\nHELLO\n+name2\n&&&!&\n'
def test_twoheaders(self):
fmt = FastqFormat()
with open_output(self.path, "w") as fw:
fw.write(fmt.format(Sequence("name", "CCATA", "!#!#!", name2="name")))
fw.write(fmt.format(Sequence("name2", "HELLO", "&&&!&", name2="name2")))
with open(self.path) as t:
assert t.read() == '@name\nCCATA\n+name\n!#!#!\n@name2\nHELLO\n+name2\n&&&!&\n'
def test(self):
fmt = FastqFormat()
with open_output(self.path, "w") as fw:
fw.write(fmt.format_entry("name", "CCATA", "!#!#!"))
fw.write(fmt.format_entry("name2", "HELLO", "&&&!&&"))
with open(self.path) as t:
assert t.read() == '@name\nCCATA\n+\n!#!#!\n@name2\nHELLO\n+\n&&&!&&\n'
def test(self):
fmt = FastqFormat()
with open_output(self.path, "w") as fw:
fw.write(fmt.format_entry("name", "CCATA", "!#!#!"))
fw.write(fmt.format_entry("name2", "HELLO", "&&&!&&"))
with open(self.path) as t:
assert t.read() == '@name\nCCATA\n+\n!#!#!\n@name2\nHELLO\n+\n&&&!&&\n'
def test(self):
reads = [
(Sequence('A/1 comment', 'TTA', '##H'),
Sequence('A/2 comment', 'GCT', 'HH#')),
(Sequence('B/1', 'CC', 'HH'),
Sequence('B/2', 'TG', '#H'))
]
fmt = InterleavedFormatter(FastqFormat(), "foo")
result = defaultdict(lambda: [])
for read1, read2 in reads:
fmt.format(result, read1, read2)
assert fmt.written == 2
assert fmt.read1_bp == 5
assert fmt.read2_bp == 5
assert "foo" in result
assert "".join(result["foo"]) == '@A/1 comment\nTTA\n+\n##H\n@A/2 comment\nGCT\n+\nHH#\n@B/1\nCC\n+\nHH\n@B/2\nTG\n+\n#H\n'