Exemplos de AnalysisSample em Python

Exemplo n.º 1

Arquivo: test_illumina_qc.py Projeto: fls-bioinformatics-core/auto_process_ngs

 def test_get_fastq_pairs_single_end(self):
     s = AnalysisSample("PB1")
     s.add_fastq("/data/PB/PB1_ATTAGG_L001_R1_001.fastq")
     s.add_fastq("/data/PB/PB1_GCCAAG_L002_R1_001.fastq")
     fq_pair = get_fastq_pairs(s)
     self.assertEqual(len(fq_pair), 2)
     self.assertEqual(fq_pair[0].r1, "/data/PB/PB1_ATTAGG_L001_R1_001.fastq")
     self.assertEqual(fq_pair[0].r2, None)
     self.assertEqual(fq_pair[1].r1, "/data/PB/PB1_GCCAAG_L002_R1_001.fastq")
     self.assertEqual(fq_pair[1].r2, None)

Exemplo n.º 2

Arquivo: test_illumina.py Projeto: pjbriggs/genomics-update-qc-reports

 def test_paired_end(self):
     s = AnalysisSample('PB1')
     s.add_fastq('/data/PB/PB1_ATTAGG_L001_R1_001.fastq')
     s.add_fastq('/data/PB/PB1_ATTAGG_L001_R2_001.fastq')
     s.add_fastq('/data/PB/PB1_GCCAAG_L002_R1_001.fastq')
     s.add_fastq('/data/PB/PB1_GCCAAG_L002_R2_001.fastq')
     self.assertEqual(get_fastq_pairs(s),[('/data/PB/PB1_ATTAGG_L001_R1_001.fastq',
                                           '/data/PB/PB1_ATTAGG_L001_R2_001.fastq'),
                                          ('/data/PB/PB1_GCCAAG_L002_R1_001.fastq',
                                           '/data/PB/PB1_GCCAAG_L002_R2_001.fastq')])

Exemplo n.º 3

Arquivo: test_illumina_qc.py Projeto: zacapte/auto_process_ngs

 def test_get_fastq_pairs_single_end(self):
     s = AnalysisSample('PB1')
     s.add_fastq('/data/PB/PB1_ATTAGG_L001_R1_001.fastq')
     s.add_fastq('/data/PB/PB1_GCCAAG_L002_R1_001.fastq')
     fq_pair = get_fastq_pairs(s)
     self.assertEqual(len(fq_pair), 2)
     self.assertEqual(fq_pair[0].r1,
                      '/data/PB/PB1_ATTAGG_L001_R1_001.fastq')
     self.assertEqual(fq_pair[0].r2, None)
     self.assertEqual(fq_pair[1].r1,
                      '/data/PB/PB1_GCCAAG_L002_R1_001.fastq')
     self.assertEqual(fq_pair[1].r2, None)

Exemplo n.º 4

Arquivo: test_illumina_qc.py Projeto: zacapte/auto_process_ngs

 def test_get_fastq_pairs_paired_end_with_index_reads(self):
     s = AnalysisSample('PB1')
     s.add_fastq('/data/PB/PB1_ATTAGG_L001_R1_001.fastq')
     s.add_fastq('/data/PB/PB1_ATTAGG_L001_R2_001.fastq')
     s.add_fastq('/data/PB/PB1_ATTAGG_L001_I1_001.fastq')
     s.add_fastq('/data/PB/PB1_GCCAAG_L002_R1_001.fastq')
     s.add_fastq('/data/PB/PB1_GCCAAG_L002_R2_001.fastq')
     s.add_fastq('/data/PB/PB1_GCCAAG_L002_I1_001.fastq')
     fq_pair = get_fastq_pairs(s)
     self.assertEqual(len(fq_pair), 2)
     self.assertEqual(fq_pair[0].r1,
                      '/data/PB/PB1_ATTAGG_L001_R1_001.fastq')
     self.assertEqual(fq_pair[0].r2,
                      '/data/PB/PB1_ATTAGG_L001_R2_001.fastq')
     self.assertEqual(fq_pair[1].r1,
                      '/data/PB/PB1_GCCAAG_L002_R1_001.fastq')
     self.assertEqual(fq_pair[1].r2,
                      '/data/PB/PB1_GCCAAG_L002_R2_001.fastq')