def test_multiple_output_files(self):
""" properly writes multiple fasta files for each sampleID"""
convert_fastq(
self.fasta_file_path,
self.qual_file_path,
multiple_output_files=True,
output_directory=self.output_dir,
per_file_buffer_size=23,
)
sample_ids = [
("PC.634", expected_fastq_634_default),
("PC.354", expected_fastq_354_default),
("PC.481", expected_fastq_481_default),
]
for sample_id, expected_output in sample_ids:
actual_output_file_path = get_filename_with_new_ext(
self.fasta_file_path, "_" + sample_id + ".fastq", self.output_dir
)
actual_output_file = open(actual_output_file_path)
actual_output = actual_output_file.read()
actual_output_file.close()
self._files_to_remove.append(actual_output_file_path)
self.assertEquals(actual_output, expected_output)
def test_full_fasta_headers(self):
""" Properly retains full fasta headers """
convert_fastq(self.fasta_file_path, self.qual_file_path, \
full_fasta_headers = True, output_directory = self.output_dir)
actual_output_file_path = self.output_dir + \
splitext(split(self.fasta_file_path)[1])[0] + '.fastq'
actual_output_file = open(actual_output_file_path)
actual_output = actual_output_file.read()
actual_output_file.close()
self._files_to_remove.append(actual_output_file_path)
self.assertEquals(actual_output, expected_fastq_full_fasta_headers)
def test_full_fasta_headers(self):
""" Properly retains full fasta headers """
convert_fastq(self.fasta_file_path, self.qual_file_path, \
full_fasta_headers = True, output_directory = self.output_dir)
actual_output_file_path = self.output_dir + \
splitext(split(self.fasta_file_path)[1])[0] + '.fastq'
actual_output_file = open(actual_output_file_path)
actual_output = actual_output_file.read()
actual_output_file.close()
self._files_to_remove.append(actual_output_file_path)
self.assertEquals(actual_output, expected_fastq_full_fasta_headers)
def test_default_settings(self):
""" Handles conversions with default settings """
convert_fastq(self.fasta_file_path, self.qual_file_path,
output_directory=self.output_dir)
actual_output_file_path = self.output_dir + \
splitext(split(self.fasta_file_path)[1])[0] + '.fastq'
actual_output_file = open(actual_output_file_path)
actual_output = actual_output_file.read()
actual_output_file.close()
self._files_to_remove.append(actual_output_file_path)
self.assertEquals(actual_output, expected_fastq_default_options)
def test_default_settings(self):
""" Handles conversions with default settings """
convert_fastq(self.fasta_file_path,
self.qual_file_path,
output_directory=self.output_dir)
actual_output_file_path = self.output_dir + \
splitext(split(self.fasta_file_path)[1])[0] + '.fastq'
actual_output_file = open(actual_output_file_path)
actual_output = actual_output_file.read()
actual_output_file.close()
self._files_to_remove.append(actual_output_file_path)
self.assertEquals(actual_output, expected_fastq_default_options)
def test_full_fasta_headers(self):
""" Properly retains full fasta headers """
convert_fastq(
self.fasta_file_path, self.qual_file_path, full_fasta_headers=True, output_directory=self.output_dir
)
actual_output_file_path = get_filename_with_new_ext(self.fasta_file_path, ".fastq", self.output_dir)
actual_output_file = open(actual_output_file_path)
actual_output = actual_output_file.read()
actual_output_file.close()
self._files_to_remove.append(actual_output_file_path)
self.assertEquals(actual_output, expected_fastq_full_fasta_headers)
def test_multiple_output_files(self):
""" properly writes multiple fasta files for each sampleID"""
convert_fastq(self.fasta_file_path, self.qual_file_path,
multiple_output_files = True, output_directory = self.output_dir)
sample_ids = [('PC.634', expected_fastq_634_default),
('PC.354', expected_fastq_354_default),
('PC.481', expected_fastq_481_default)]
for sample_id, expected_output in sample_ids:
actual_output_file_path = self.output_dir + \
splitext(split(self.fasta_file_path)[1])[0] +'_%s.fastq' %\
sample_id
actual_output_file = open(actual_output_file_path)
actual_output = actual_output_file.read()
actual_output_file.close()
self._files_to_remove.append(actual_output_file_path)
self.assertEquals(actual_output, expected_output)
def test_multiple_output_files(self):
""" properly writes multiple fasta files for each sampleID"""
convert_fastq(self.fasta_file_path,
self.qual_file_path,
multiple_output_files=True,
output_directory=self.output_dir)
sample_ids = [('PC.634', expected_fastq_634_default),
('PC.354', expected_fastq_354_default),
('PC.481', expected_fastq_481_default)]
for sample_id, expected_output in sample_ids:
actual_output_file_path = self.output_dir + \
splitext(split(self.fasta_file_path)[1])[0] +'_%s.fastq' %\
sample_id
actual_output_file = open(actual_output_file_path)
actual_output = actual_output_file.read()
actual_output_file.close()
self._files_to_remove.append(actual_output_file_path)
self.assertEquals(actual_output, expected_output)
