def setup(self):
thisdir = os.path.dirname(__file__)
self._fileName = os.path.join(thisdir, 'fastqRecovery')
self._testfq = os.path.join(thisdir, 'test.fastq')
screed.read_fastq_sequences(self._testfq)
screed.ToFastq(self._testfq, self._fileName)
screed.read_fastq_sequences(self._fileName)
self.db = screed.ScreedDB(self._fileName)
def setup(self):
self._fileName = utils.get_temp_filename('fastqRecovery')
self._testfq = utils.get_temp_filename('test.fastq')
shutil.copy(utils.get_test_data('test.fastq'), self._testfq)
screed.read_fastq_sequences(self._testfq)
screed.ToFastq(self._testfq, self._fileName)
screed.read_fastq_sequences(self._fileName)
self.db = screed.ScreedDB(self._fileName)
def setup(self):
thisdir = os.path.dirname(__file__)
self._fqName = os.path.join(thisdir, 'fa_to_fq')
self._faName = os.path.join(thisdir, 'fq_to_fa')
self._testfa = os.path.join(thisdir, 'test.fa')
screed.read_fasta_sequences(self._testfa)
screed.ToFastq(self._testfa, self._fqName) # Fasta db -> fasta text
screed.read_fastq_sequences(self._fqName) # Fastq file -> fastq db
screed.ToFasta(self._fqName, self._faName) # Fastq db -> fasta text
screed.read_fasta_sequences(self._faName) # Fasta file -> fasta db
self.db = screed.ScreedDB(self._faName)
def setup(self):
self._fqName = utils.get_temp_filename('fa_to_fq')
self._faName = utils.get_temp_filename('fq_to_fa')
self._testfa = utils.get_temp_filename('test.fa')
shutil.copy(utils.get_test_data('test.fa'), self._testfa)
screed.read_fasta_sequences(self._testfa)
screed.ToFastq(self._testfa, self._fqName) # Fasta db -> fasta text
screed.read_fastq_sequences(self._fqName) # Fastq file -> fastq db
screed.ToFasta(self._fqName, self._faName) # Fastq db -> fasta text
screed.read_fasta_sequences(self._faName) # Fasta file -> fasta db
self.db = screed.ScreedDB(self._faName)