def test_runs( self ):
from bactpipeline.runsample import flash
flashout = flash( *self.fqs )
inf = flashout[0]
outf = inf.replace('.fastq','.btrim.fastq')
r = self._C( p=self.truseq, t=inf, o=outf, b=300, c=True, Q=True, S=True, l=100 )
ok_( exists(outf), 'btrim did not create {0}'.format(outf) )
ok_( os.stat(inf).st_size != os.stat(outf).st_size, 'Did not trim input file. Input and output file are same size still' )
def flash( self, prefix='out', outdir='flash' ):
from bactpipeline.runsample import flash
# Files from flash
return [f for f in flash( *self.fqs, d=outdir, o=prefix ) if f.endswith('.fastq')]
def _C( self, *args, **kwargs ):
from bactpipeline.runsample import flash
return flash( *args, **kwargs )
def test_returns_retcode( self ):
from bactpipeline.runsample import flash
flashout = flash( *self.fqs )
eq_( 0, self._C( p=self.truseq, t=flashout[0], o='somefile' ), 'Did not return return code' )
r = self._C()
ok_( 0 != r, 'btrim return code was {0} instead of non-zero'.format(r) )