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)
Exemplo n.º 2
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    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)
Exemplo n.º 5
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    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) 
Exemplo n.º 8
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    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)