def test_multiple_output_files(self):
""" Creates one file per sampleID for fasta/qual output """
convert_fastaqual(
self.fasta_file_path, multiple_output_files=True, output_directory=self.output_dir, per_file_buffer_size=23
)
sample_id_s = [
("PC.634", expected_fasta_634_default, expected_qual_634_default),
("PC.354", expected_fasta_354_default, expected_qual_354_default),
("PC.481", expected_fasta_481_default, expected_qual_481_default),
]
for sample_id, expected_fasta, expected_qual in sample_id_s:
actual_output_fasta_path = get_filename_with_new_ext(
self.fasta_file_path, "_" + sample_id + ".fna", self.output_dir
)
actual_output_qual_path = get_filename_with_new_ext(
self.fasta_file_path, "_" + sample_id + ".qual", self.output_dir
)
actual_output_fasta = open(actual_output_fasta_path)
actual_output_qual = open(actual_output_qual_path)
actual_fasta = actual_output_fasta.read()
actual_output_fasta.close()
actual_qual = actual_output_qual.read()
actual_output_qual.close()
self._files_to_remove.append(actual_output_fasta_path)
self._files_to_remove.append(actual_output_qual_path)
self.assertEquals(actual_fasta, expected_fasta)
self.assertEquals(actual_qual, expected_qual)
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):
""" Full headers written to fasta/qual files """
convert_fastaqual(self.fasta_file_path, full_fasta_headers=True, output_directory=self.output_dir)
actual_output_fasta_path = get_filename_with_new_ext(self.fasta_file_path, ".fna", self.output_dir)
actual_output_qual_path = get_filename_with_new_ext(self.fasta_file_path, ".qual", self.output_dir)
actual_output_fasta = open(actual_output_fasta_path)
actual_output_qual = open(actual_output_qual_path)
actual_fasta = actual_output_fasta.read()
actual_output_fasta.close()
actual_qual = actual_output_qual.read()
actual_output_qual.close()
self._files_to_remove.append(actual_output_fasta_path)
self._files_to_remove.append(actual_output_qual_path)
self.assertEquals(actual_fasta, expected_fasta_full_fasta_headers)
self.assertEquals(actual_qual, expected_qual_full_fasta_headers)
def test_default_settings(self):
""" Converting to fasta/qual files handles default settings """
convert_fastaqual(self.fasta_file_path, output_directory=self.output_dir)
actual_output_fasta_path = get_filename_with_new_ext(self.fasta_file_path, ".fna", self.output_dir)
actual_output_qual_path = get_filename_with_new_ext(self.fasta_file_path, ".qual", self.output_dir)
actual_output_fasta = open(actual_output_fasta_path)
actual_output_qual = open(actual_output_qual_path)
actual_fasta = actual_output_fasta.read()
actual_output_fasta.close()
actual_qual = actual_output_qual.read()
actual_output_qual.close()
self._files_to_remove.append(actual_output_fasta_path)
self._files_to_remove.append(actual_output_qual_path)
self.assertEquals(actual_fasta, expected_fasta_default_options)
self.assertEquals(actual_qual, expected_qual_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 = 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_default_options)
def test_get_filename_with_new_ext(self):
""" Tests proper function of the utility function. """
test_paths = [
("/from/root/test.xxx", "test.yyy"),
("../relative/path/test.xxx", "test.yyy"),
("/double/extension/in/filename/test.zzz.xxx", "test.zzz.yyy"),
]
for input, exp_output in test_paths:
exp_output = join(self.output_dir, exp_output)
self.assertEquals(get_filename_with_new_ext(input, ".yyy", self.output_dir), exp_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 = 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)
