Python prepare_input_data Beispiele

Beispiel #1

Datei: test_ericscript.py Projekt: biocyberman/bcbio-nextgen

 def test_get_fastq_input_files_if_no_disambiguation(self):
     fq_files = (
         '/path/to/1_1_trimmed.fq.gz',
         '/path/to/1_2_trimmed.fq.gz'
     )
     sample_config = {'files': list(fq_files)}
     result = ericscript.prepare_input_data(sample_config)
     assert result == fq_files

Beispiel #2

Datei: test_ericscript.py Projekt: limbus-medtec/bcbio-nextgen-1

 def test_get_fastq_input_files_if_no_disambiguation(self):
     fq_files = (
         '/path/to/1_1_trimmed.fq.gz',
         '/path/to/1_2_trimmed.fq.gz'
     )
     sample_config = {'files': list(fq_files)}
     result = ericscript.prepare_input_data(sample_config)
     assert result == fq_files

Beispiel #3

    def test_get_disambiguated_bam(self, mocker):
        sample_config = {
            'config': {
                'algorithm': {
                    'disambiguate': ['mm9'],
                }
            },
            'work_bam':
            '/path/to/disambiguate_star/Test1.nsorted.human.sorted.bam',
            'dirs': {
                'work': '/path/to/workdir'
            },
        }

        convert = mocker.patch('bcbio.rnaseq.ericscript.convert_bam_to_fastq')
        result = ericscript.prepare_input_data(sample_config)
        convert.assert_called_once_with(sample_config['work_bam'],
                                        sample_config['dirs']['work'], None,
                                        None, sample_config)
        assert result == convert.return_value

Beispiel #4

Datei: test_ericscript.py Projekt: biocyberman/bcbio-nextgen

    def test_get_disambiguated_bam(self, mocker):
        sample_config = {
            'config': {
                'algorithm': {
                    'disambiguate': ['mm9'],
                }
            },
            'work_bam':
                '/path/to/disambiguate_star/Test1.nsorted.human.sorted.bam',
            'dirs': {'work': '/path/to/workdir'},
        }

        convert = mocker.patch('bcbio.rnaseq.ericscript.convert_bam_to_fastq')
        result = ericscript.prepare_input_data(sample_config)
        convert.assert_called_once_with(
            sample_config['work_bam'],
            sample_config['dirs']['work'],
            None, None, sample_config
        )
        assert result == convert.return_value