def test_set_outdir(self):
args = ['ReadsBySample', 'Reference.fasta', 'Sample1', '-od', 'outdir']
res = runsample.parse_args(args)
eq_('ReadsBySample', res[0].readsdir)
eq_('Reference.fasta', res[0].reference)
eq_('Sample1', res[0].prefix)
eq_('outdir', res[0].outdir)
def test_defaults(self):
args = ['ReadsBySample', 'Reference.fasta', 'Sample1']
res = runsample.parse_args(args)
eq_('ReadsBySample', res[0].readsdir)
eq_('Reference.fasta', res[0].reference)
eq_('Sample1', res[0].prefix)
eq_(os.getcwd(), res[0].outdir)
def test_set_outdir( self ):
args = ['ReadsBySample','Reference.fasta','Sample1','-od','outdir']
res = runsample.parse_args( args )
eq_( 'ReadsBySample', res[0].readsdir )
eq_( 'Reference.fasta', res[0].reference )
eq_( 'Sample1', res[0].prefix )
eq_( 'outdir', res[0].outdir )
def test_defaults( self ):
args = ['ReadsBySample','Reference.fasta','Sample1']
res = runsample.parse_args( args )
eq_( 'ReadsBySample', res[0].readsdir )
eq_( 'Reference.fasta', res[0].reference )
eq_( 'Sample1', res[0].prefix )
eq_( os.getcwd(), res[0].outdir )
def test_drop_ns_bool(self):
args = [
'ReadsBySample', 'Reference.fasta', 'Sample1', '-od', 'outdir',
'--drop-ns'
]
res = runsample.parse_args(args)
args, qsub_args = res
eq_(args.drop_ns, True)
def test_drop_ns_bool(self):
args = [
'ReadsBySample','Reference.fasta','Sample1',
'-od','outdir', '--drop-ns'
]
res = runsample.parse_args(args)
args, qsub_args = res
eq_(args.drop_ns, True)
def test_parses_qsub_args(self):
args = [
'ReadsBySample', 'Reference.fasta', 'Sample1', '-od', 'outdir',
'--qsub_M', 'foo'
]
res = runsample.parse_args(args)
args, qsub_args = res
eq_(args.outdir, 'outdir')
eq_(qsub_args.qsub_M, 'foo')
def test_parses_qsub_args(self):
args = [
'ReadsBySample','Reference.fasta','Sample1',
'-od','outdir', '--qsub_M', 'foo'
]
res = runsample.parse_args(args)
args, qsub_args = res
eq_(args.outdir, 'outdir')
eq_(qsub_args.qsub_M, 'foo')