How to use the cutadapt.seqio.FastaWriter function in cutadapt

To help you get started, we’ve selected a few cutadapt examples, based on popular ways it is used in public projects.

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

github marcelm / cutadapt / tests / test_seqio.py View on Github external
def test(self):
		with FastaWriter(self.path) as fw:
			fw.write("name", "CCATA")
			fw.write("name2", "HELLO")
		assert fw._file.closed
		with open(self.path) as t:
			assert t.read() == '>name\nCCATA\n>name2\nHELLO\n'
github marcelm / cutadapt / tests / test_seqio.py View on Github external
def test_write_sequence_object(self):
		with FastaWriter(self.path) as fw:
			fw.write(Sequence("name", "CCATA"))
			fw.write(Sequence("name2", "HELLO"))
		assert fw._file.closed
		with open(self.path) as t:
			assert t.read() == '>name\nCCATA\n>name2\nHELLO\n'
github marcelm / cutadapt / tests / test_seqio.py View on Github external
def test_write_zero_length_sequence(self):
		sio = StringIO()
		with FastaWriter(sio) as fw:
			fw.write(Sequence("name", ""))
			assert sio.getvalue() == '>name\n\n', '{0!r}'.format(sio.getvalue())
github marcelm / cutadapt / tests / test_seqio.py View on Github external
def test_write_to_file_like_object(self):
		sio = StringIO()
		with FastaWriter(sio) as fw:
			fw.write(Sequence("name", "CCATA"))
			fw.write(Sequence("name2", "HELLO"))
			assert sio.getvalue() == '>name\nCCATA\n>name2\nHELLO\n'
		assert not fw._file.closed
github marcelm / cutadapt / tests / test_seqio.py View on Github external
def test_linelength(self):
		with FastaWriter(self.path, line_length=3) as fw:
			fw.write("r1", "ACG")
			fw.write("r2", "CCAT")
			fw.write("r3", "TACCAG")
		assert fw._file.closed
		with open(self.path) as t:
			d = t.read()
			assert d == '>r1\nACG\n>r2\nCCA\nT\n>r3\nTAC\nCAG\n'
github marcelm / cutadapt / tests / test_seqio.py View on Github external
def test_autodetect_fasta_format(self):
		path = os.path.join(self._tmpdir, 'tmp.fasta')
		with openseq(path, mode='w') as f:
			assert isinstance(f, FastaWriter)
			for seq in simple_fastq:
				f.write(seq)
		assert list(openseq(path)) == simple_fasta
github marcelm / cutadapt / tests / test_seqio.py View on Github external
def test_write_qualities_to_fasta(self):
		path = os.path.join(self._tmpdir, 'tmp.fasta')
		with openseq(path, mode='w', qualities=True) as f:
			assert isinstance(f, FastaWriter)
			for seq in simple_fastq:
				f.write(seq)
		assert list(openseq(path)) == simple_fasta