def test_main_index_bam(self, tmpdir, tasic2016_unprocessed, bam_filenames,
tasic2016_outrigger_output_bam):
from outrigger.commandline import CommandLine
output_folder = tmpdir.strpath
gtf = os.path.join(tasic2016_unprocessed, 'gtf',
'gencode.vM10.annotation.subset.gtf')
arguments = ['index', '--bam']
arguments.extend(bam_filenames)
arguments.extend(['--gtf', gtf, '--output', output_folder])
# import pdb; pdb.set_trace()
# assert False
CommandLine(arguments)
dir1 = os.path.join(output_folder, 'index')
dir2 = os.path.join(tasic2016_outrigger_output_bam, 'index')
ignore = [
'psi',
'.DS_Store',
'validated',
'splice_sites.csv',
# Databases get stored in a weird random way... we're still
# checking that the final gtfs are the same
'gencode.vM10.annotation.subset.gtf.db'
]
assert_directories_equal(dir1, dir2, ignore)
def test_main_psi_parallelized(self, tmpdir, tasic2016_unprocessed,
tasic2016_outrigger_output, sj_filenames):
from outrigger.commandline import CommandLine
output_folder = tmpdir.strpath
gtf = os.path.join(tasic2016_unprocessed, 'gtf',
'gencode.vM10.annotation.subset.gtf')
arguments = ['index', '--sj-out-tab']
arguments.extend(sj_filenames)
arguments.extend(['--gtf', gtf, '--output', output_folder])
CommandLine(arguments)
args = ['psi', '--output', output_folder, '--n-jobs', '-1']
CommandLine(args)
dir1 = output_folder
dir2 = tasic2016_outrigger_output
assert_directories_equal(dir1, dir2, ignore=['.DS_Store'])
def test_main_version(self, capsys):
from outrigger.commandline import CommandLine
from outrigger import __version__
with pytest.raises(SystemExit):
CommandLine(['--version'])
out, err = capsys.readouterr()
# Argparse for Python2 sends the version info to stderr, but Python3
# argparse sends the info to stdout so we concatenate here
outerr = out + err
assert 'outrigger' in outerr
assert __version__ in outerr
def test_help(self, capsys):
"""
User asks for help, should SystemExit and give helpful output
"""
from outrigger.commandline import CommandLine
with pytest.raises(SystemExit):
CommandLine(['--help'])
out, err = capsys.readouterr()
assert 'outrigger' in out
assert 'psi' in out
assert 'validate' in out
assert 'usage' in out
def test_main_psi_bam(self, tmpdir, tasic2016_outrigger_output_index,
tasic2016_outrigger_output_bam, bam_filenames):
from outrigger.commandline import CommandLine
output_folder = tmpdir.strpath
args = [
'psi', '--output', output_folder, '--n-jobs', '1', '--index',
tasic2016_outrigger_output_index, '--bam'
]
args.extend(bam_filenames)
CommandLine(args)
dir1 = output_folder
dir2 = tasic2016_outrigger_output_bam
assert_directories_equal(dir1, dir2, ignore=['.DS_Store', 'index'])
def test_no_arguments(self, capsys):
"""
User passes no args, should fail with SystemExit
"""
from outrigger.commandline import CommandLine
CommandLine()
text = '[-h] [--version] {index,validate,psi} ...'
out, err = capsys.readouterr()
# Argparse for Python2 sends the version info to stderr, but Python3
# argparse sends the info to stdout so we concatenate here
outerr = out + err
assert 'usage' in outerr
assert text in outerr
def test_main_validate(self, tmpdir, negative_control_folder,
negative_control_output):
from outrigger.commandline import CommandLine
args = [
'validate', '--genome',
'{folder}/chromsizes'.format(folder=negative_control_folder),
'--fasta',
'{folder}/genome.fasta'.format(folder=negative_control_folder),
'--output', tmpdir.strpath, '--index',
os.path.join(negative_control_output, 'index')
]
CommandLine(args)
dir1 = tmpdir.strpath
dir2 = negative_control_output
assert_directories_equal(dir1,
dir2,
ignore=['.DS_Store', 'junctions', 'gtf'])
