Python main Examples

Example #1

File: test_sequence_split.py Project: averagehat/bio_pieces

 def test_F_fastq_compiled_correct_record_number(self, m_parse_args):
     m_parse_args.return_value = self.default_args
     sequence_split.main()
     for filename, expected_num_records in self.yield_files_and_lengths(
             'fastq'):
         result_records = list(SeqIO.parse(filename, 'fastq'))
         self.assertEquals(expected_num_records, len(result_records))

Example #2

File: test_sequence_split.py Project: averagehat/bio_pieces

    def test_F_fastq_to_fasta_some_lines_exist(self, m_parse_args):
        m_parse_args.return_value =  Namespace(seqfile='tests/F.fastq', delimiter=':', file_type='fastq', outdir=self.outdir, out_format='fasta', colnum=1)
        sequence_split.main()
        expected_lines = [">M02261:C1:000000000-A648D:1:1101:17702:1010 1:N:0:84",
"NCTTGGCGTAAAGGCAGTGATTGCCGAGAGCTTTGAGCGAATACATCGTTCAAATTTAGTTGGTATGGGTATTTTACCGCTAACTTTNACCGGNNNNAATNCAAGATTAGATTTAAAGTTAGACGGTTCGGAAACTATTGATATTATAGGCTTAAGTGAACAAATAAAGCCTTATAATCCTGTTAAATGCATGATAA", ">M02261:C1:000000000-A648D:1:1101:15313:1016 1:N:0:84"," NAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAANAGAAGNNAANAGAAGAGAAGAGAAGAGAGAAGAGGAGAGACA"]
        expected = ''.join(expected_lines).replace(' ', '')
        self.assertTrue(expected in open(os.path.join(self.outdir, 'C1.fasta')).read().replace('\n', '').replace(' ', ''))

Example #3

File: test_sequence_split.py Project: averagehat/bio_pieces

 def test_F_fastq_to_fasta_files_exist(self, m_parse_args):
     m_parse_args.return_value = Namespace(seqfile='tests/F.fastq',
                                           delimiter=':',
                                           file_type='fastq',
                                           outdir=self.outdir,
                                           out_format='fasta',
                                           colnum=1)
     sequence_split.main()
     for filename, _ in self.yield_files_and_lengths('fasta'):
         self.assertTrue(os.path.isfile(filename))

Example #4

File: test_sequence_split.py Project: averagehat/bio_pieces

 def test_F_fastq_to_fasta_num_records(self, m_parse_args):
     m_parse_args.return_value = Namespace(seqfile='tests/F.fastq',
                                           delimiter=':',
                                           file_type='fastq',
                                           outdir=self.outdir,
                                           out_format='fasta',
                                           colnum=1)
     sequence_split.main()
     for filename, num_records in self.yield_files_and_lengths('fasta'):
         result_records = list(SeqIO.parse(filename, 'fasta'))
         self.assertEquals(num_records, len(result_records))

Example #5

File: test_sequence_split.py Project: averagehat/bio_pieces

 def test_F_fastq_to_fasta_some_lines_exist(self, m_parse_args):
     m_parse_args.return_value = Namespace(seqfile='tests/F.fastq',
                                           delimiter=':',
                                           file_type='fastq',
                                           outdir=self.outdir,
                                           out_format='fasta',
                                           colnum=1)
     sequence_split.main()
     expected_lines = [
         ">M02261:C1:000000000-A648D:1:1101:17702:1010 1:N:0:84",
         "NCTTGGCGTAAAGGCAGTGATTGCCGAGAGCTTTGAGCGAATACATCGTTCAAATTTAGTTGGTATGGGTATTTTACCGCTAACTTTNACCGGNNNNAATNCAAGATTAGATTTAAAGTTAGACGGTTCGGAAACTATTGATATTATAGGCTTAAGTGAACAAATAAAGCCTTATAATCCTGTTAAATGCATGATAA",
         ">M02261:C1:000000000-A648D:1:1101:15313:1016 1:N:0:84",
         " NAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAANAGAAGNNAANAGAAGAGAAGAGAAGAGAGAAGAGGAGAGACA"
     ]
     expected = ''.join(expected_lines).replace(' ', '')
     self.assertTrue(expected in open(os.path.join(self.outdir, 'C1.fasta'))
                     .read().replace('\n', '').replace(' ', ''))

Example #6

File: test_sequence_split.py Project: averagehat/bio_pieces

 def test_F_fastq_compiled_correct_record_number(self, m_parse_args):
     m_parse_args.return_value = self.default_args
     sequence_split.main()
     for filename, expected_num_records in self.yield_files_and_lengths('fastq'):
         result_records = list(SeqIO.parse(filename, 'fastq'))
         self.assertEquals(expected_num_records, len(result_records) )

Example #7

File: test_sequence_split.py Project: averagehat/bio_pieces

 def test_F_fastq_to_fasta_num_records(self, m_parse_args):
     m_parse_args.return_value =  Namespace(seqfile='tests/F.fastq', delimiter=':', file_type='fastq', outdir=self.outdir, out_format='fasta', colnum=1)
     sequence_split.main()
     for filename, num_records in self.yield_files_and_lengths('fasta'):
         result_records = list(SeqIO.parse(filename, 'fasta'))
         self.assertEquals(num_records, len(result_records))

Example #8

File: test_sequence_split.py Project: averagehat/bio_pieces

 def test_F_fastq_to_fasta_files_exist(self, m_parse_args):
     m_parse_args.return_value =  Namespace(seqfile='tests/F.fastq', delimiter=':', file_type='fastq', outdir=self.outdir, out_format='fasta', colnum=1)
     sequence_split.main()
     for filename, _ in self.yield_files_and_lengths('fasta'):
         self.assertTrue(os.path.isfile(filename))

Example #9

File: test_sequence_split.py Project: averagehat/bio_pieces

 def test_F_fastq_compiled_files_exist(self, m_parse_args):
     m_parse_args.return_value = self.default_args
     sequence_split.main()
     for filename, _ in self.yield_files_and_lengths('fastq'):
         self.assertTrue(os.path.isfile(filename))

Example #10

File: test_sequence_split.py Project: averagehat/bio_pieces

 def test_F_fastq_compiled_files_exist(self, m_parse_args):
     m_parse_args.return_value = self.default_args
     sequence_split.main()
     for filename, _ in self.yield_files_and_lengths('fastq'):
         self.assertTrue(os.path.isfile(filename))