outrigger.tests.test_commandline module¶

class outrigger.tests.test_commandline.TestCommandLine[source]¶

Bases: object

Methods

`test_help`(capsys)	User asks for help, should SystemExit and give helpful output
`test_main_index`(tmpdir, ...)
`test_main_index_bam`(tmpdir, ...)
`test_main_index_parallelized`(tmpdir, ...)
`test_main_index_reads_csv`(tmpdir, ...)
`test_main_psi`(tmpdir, tasic2016_unprocessed, ...)
`test_main_psi_bam`(tmpdir, ...)
`test_main_psi_parallelized`(tmpdir, ...)
`test_main_validate`(tmpdir, ...)
`test_main_version`(capsys)
`test_no_arguments`(capsys)	User passes no args, should fail with SystemExit

test_help(capsys)[source]¶: User asks for help, should SystemExit and give helpful output

test_main_index(tmpdir, tasic2016_unprocessed, sj_filenames, tasic2016_outrigger_output_index)[source]¶

test_main_index_bam(tmpdir, tasic2016_unprocessed, bam_filenames, tasic2016_outrigger_output_bam)[source]¶

test_main_index_parallelized(tmpdir, tasic2016_unprocessed, sj_filenames, tasic2016_outrigger_output_index)[source]¶

test_main_index_reads_csv(tmpdir, tasic2016_unprocessed, tasic2016_outrigger_output, tasic2016_outrigger_output_index)[source]¶

test_main_psi(tmpdir, tasic2016_unprocessed, tasic2016_outrigger_output, sj_filenames)[source]¶

test_main_psi_bam(tmpdir, tasic2016_outrigger_output_index, tasic2016_outrigger_output_bam, bam_filenames)[source]¶

test_main_psi_parallelized(tmpdir, tasic2016_unprocessed, tasic2016_outrigger_output, sj_filenames)[source]¶

test_main_validate(tmpdir, negative_control_folder, negative_control_output)[source]¶

test_no_arguments(capsys)[source]¶: User passes no args, should fail with SystemExit

class outrigger.tests.test_commandline.TestSubcommand[source]¶

Bases: object

Methods

test___init__(tmpdir)

outrigger.tests.test_commandline.assert_directories_equal(dir1, dir2, ignore=None, sortables=('exon', 'junction'))[source]¶: Compare contents of subdirectories to assert they are equal