def setUp(self):
RnaseqGlobals.initialize(__file__, testing=True)
templated.template_dir=RnaseqGlobals.root_dir()+"/t/fixtures/templates"
readset_file=RnaseqGlobals.root_dir()+"/t/fixtures/readsets/readset1.syml"
self.readset=Readset.load(readset_file)[0]
self.pipeline=Pipeline(name='juan', readset=self.readset).load_steps()
session=RnaseqGlobals.get_session()
# delete all pre-existing pipeline objects from the db:
plist=session.query(Pipeline)
for p in plist:
session.delete(p)
session.commit()
def setUp(self):
templated.template_dir=os.path.normpath(os.path.abspath(__file__)+"/../../fixtures/templates")
RnaseqGlobals.initialize(__file__, testing=True)
RnaseqGlobals.set_conf_value('force',True)
RnaseqGlobals.set_conf_value('silent',True)
readset=Readset.load(RnaseqGlobals.root_dir()+'/t/fixtures/readsets/readset1.syml')[0]
self.pipeline=Pipeline(name='filter', readset=readset)
def setUp(self):
RnaseqGlobals.initialize(__file__, testing=True)
templated.template_dir=RnaseqGlobals.root_dir()+'/t/fixtures/templates'
os.chdir(RnaseqGlobals.root_dir()+'/t/fixtures/readsets')
filename=RnaseqGlobals.root_dir()+'/t/fixtures/readsets/readset_rel_glob.syml'
rlist=Readset.load(filename)
readset=rlist[0]
self.readset=readset
self.session=RnaseqGlobals.get_session()
rlist=self.session.query(Readset)
for rs in rlist:
self.session.delete(rs)
self.session.commit()
def setUp(self):
templated.template_dir=os.path.normpath(os.path.abspath(__file__)+"/../../fixtures/templates")
RnaseqGlobals.initialize(__file__, testing=True)
readset_file=RnaseqGlobals.root_dir()+'/t/fixtures/readsets/paired1.syml'
self.readset=Readset.load(filename=readset_file)[0]
self.pipeline=Pipeline(name='test_newstep', readset=self.readset)
def sh_script(self, context, **args):
if 'echo_name' in args and args['echo_name']:
echo_part="\n# step %s:\n" % self.name
echo_part+="echo step %s 1>&2" % self.name
else:
echo_part=''
try: usage=self.usage(context)
except KeyError as ke:
raise ConfigError("missing config item '%s'" % ke)
# check for missing attrs after calling step.usage()
missing_attrs=self.missing_required_attrs()
if len(missing_attrs) > 0:
raise ConfigError("step %s: missing attributes: %s" % (self.name, ', '.join(missing_attrs)))
vars={}
vars.update(self.__dict__)
vars.update(self.pipeline.readset)
if not self.is_prov_step:
vars.update(self.pipeline[self.name])
vars['inputs']=context.inputs[self.name]
vars['outputs']=context.outputs[self.name]
vars['pipeline']=self.pipeline
vars['pipeline_run_id']=context.pipeline_run_id
#vars['step_run_id']=context.step_runs[self.name].id
#vars['next_step_run_id']=context.step_runs[self.pipeline.step_after(step.name)].id
vars['config']=RnaseqGlobals.config
vars['readset']=self.pipeline.readset
# need to add shell variables for 'set': (in cufflinks.s_?.sh scripts)
# currently root_dir, programs, reads_file, ID, format, readlen
# but really, the pipeline should specify these?
# or only things that are truly universal
vars['root_dir']=RnaseqGlobals.root_dir()
# add readset exports:
readset=self.pipeline.readset
for attr in readset.exports:
try: vars[attr]=getattr(readset, attr)
except AttributeError:
vars[attr]=''
#warn("%s.sh_script: no '%s' readset attribute!" % (self.name, attr))
# add self.exports:
try: export_list=self.exports
except: export_list=[]
for attr in export_list:
vars[attr]=getattr(self,attr)
try: script_part=evoque_template(usage, vars)
except Exception as e: raise ConfigError("step %s: %s" % (self.name, e))
script="\n".join([echo_part,script_part]) # tried using echo_part+sh_script, got weird '>' -> '>' substitutions
return script
def test_list(self):
readset_file=RnaseqGlobals.root_dir()+'/t/fixtures/readsets/readset12.syml'
rlist=Readset.load(readset_file)
self.assertEqual(type(rlist),type([]))
self.assertEqual(len(rlist),6)
for rs in rlist:
self.assertEqual(rs.org, 'mouse')
self.assertEqual(rs.readlen, 75)
self.assertEqual(os.path.dirname(rs.reads_file), self.readset_dir)
self.assertTrue(re.match('s_\d\d?_\d_sequence.txt',os.path.basename(rs.reads_file)))
self.assertTrue(re.search(rs.label,os.path.basename(rs.reads_file)))
self.assertEqual(rs.label,rs.description)
def setUp(self):
templated.template_dir=os.path.normpath(os.path.abspath(__file__)+"/../../fixtures/templates")
RnaseqGlobals.initialize(__file__, testing=True)
readset_file=os.path.join(RnaseqGlobals.root_dir(),'t','fixtures','readsets','readset1.syml')
self.readset=Readset.load(readset_file)[0]
self.pipeline=Pipeline(name='juan', readset=self.readset).load_steps()
session=RnaseqGlobals.get_session()
ps=session.query(Pipeline).all()
for p in ps:
session.delete(p)
session.commit()
def test_glob_rel(self):
readset_file=RnaseqGlobals.root_dir()+'/t/fixtures/readsets/readset_rel_glob.syml'
rlist=Readset.load(readset_file)
self.assertEqual(len(rlist),1)
filelist=rlist[0].reads_files
self.assertEqual(len(filelist), 3)
for i in range(1,3):
filename="s_%d_export.txt" % i
found=False
for f in filelist:
if re.search(filename, f):
found=True
break
self.assertTrue(found)
def verify_exe(self):
if not hasattr(self,'exe'): return True
dir_list=RnaseqGlobals.conf_value('rnaseq', 'path').split(":")
dir_list.extend([os.path.join(RnaseqGlobals.root_dir(),'programs')])
if exists_on_path(self.exe, dir_list, os.X_OK): return True
# didn't find executable directly, see if there's an interpreter:
if hasattr(self,'interpreter'):
return exists_on_path(self.interpreter, dir_list, os.X_OK) and \
exists_on_path(self.exe, dir_list, os.R_OK)
# couldn't find self.exe, no self.interpreter:
return False
def test_dict(self):
dir=RnaseqGlobals.root_dir()+'/t/fixtures/readsets'
os.chdir(dir)
filename=os.path.join(dir,'readset_rel_glob.syml')
rlist=Readset.load(filename)
readset=rlist[0]
self.assertRegexpMatches(readset['reads_file'], dir+'/s_\d_export.txt')
self.assertEqual(readset['description'],'this is a sample readset (fixture)')
self.assertEqual(readset['org'],'mouse')
self.assertEqual(readset['readlen'],75)
self.assertEqual(readset['working_dir'],os.path.join(dir,'rnaseq_wf'))
vars={'this': 'that'}
readset.update(vars)
self.assertEqual(readset['this'],'that')
def setUp(self):
templated.template_dir=os.path.normpath(os.path.abspath(__file__)+"/../../fixtures/templates")
RnaseqGlobals.initialize(__file__, testing=True)
self.readset=Readset.load(RnaseqGlobals.root_dir()+'/t/fixtures/readsets/readset1.syml')[0]
def setUp(self):
RnaseqGlobals.initialize(__file__, testing=True)
#templated.template_dir=RnaseqGlobals.root_dir()+"/../../fixtures/templates"
self.readset_dir=os.path.join(RnaseqGlobals.root_dir(),'t/fixtures/readsets')
