def test_step_scripts(self):
script_file=os.path.join(RnaseqGlobals.root_dir(),'t/fixtures/sh_scripts/cufflinks.sh')
expected=fragment_script(script_file)
for step in self.pipeline.steps:
if step.name=='header': continue
step_script=step.sh_script(self.pipeline.context, echo_name=True).strip()
fd=first_diff(step_script, expected[step.name])
if fd >= 0:
print "%s: first diff at %d" % (step.name, fd)
(d1,d2)=diff_strs(step_script, expected[step.name])
print "%s diff:\ngenerated: %s\nexpected: %s" % (step.name, d1, d2)
self.assertEqual(step_script, expected[step.name])
def test_sh_cmd(self):
step=self.pipeline.step_with_name('remove_erccs')
self.assertNotEqual(step, None)
try:
script=step.sh_script(self.pipeline.context)
except Exception as e:
print "test_align_filter: caught %s (%s)" % (e, type(e))
self.fail()
expected='''
export BOWTIE_INDEXES=/proj/hoodlab/share/programs/RNAseq-Pi/data/bowtie-indexes
bowtie ERCC_reference_081215 -1 ${ID}_1.${format} -2 ${ID}_2.${format} --quiet -p 4 -S --sam-nohead -k 1 -v 2 -q | perl -lane 'print unless($F[1] == 4)' > ${ID}.remove_erccs_BAD.${format}
'''
fd=first_diff(script, expected)
if fd >= 0:
print "%s: first diff at %d" % (step.name, fd)
(d1,d2)=diff_strs(script, expected)
print "%s diff:\ngenerated: %s\nexpected: %s" % (step.name, d1, d2)
self.assertEqual(script,expected)