def run(self):
'It runs the analysis.'
inputs, output_dirs = self._get_inputs_and_prepare_outputs()
db_dir = output_dirs['db_dir']
result_dir = output_dirs['result']
blast_settings = self._project_settings['blast']
go_settings = self._project_settings['Annotation']['go_annotation']
go_database = go_settings['blast_database']
create_dat = go_settings['create_dat_file']
java_memory = go_settings['java_memory']
prop_fpath = go_settings['b2g_properties_file']
if not prop_fpath:
msg = 'Blast2go properties file path not given in backbone.conf'
raise ValueError(msg)
blast2go_path = go_settings['blast2go_path']
if not blast2go_path:
msg = 'Path to blast2go binary not given in backbone.conf'
raise ValueError(msg)
blast2go = {}
for input_ in inputs['input']:
input_fpath = input_.last_version
annot_fpath = join(result_dir, input_.basename + '.b2g.annot')
if not exists(annot_fpath):
go_blast_settings = blast_settings[go_database]
blast = self._get_b2g_blast(input_fpath, go_blast_settings)
if create_dat:
dat_fpath = join(result_dir, input_.basename + '.b2g.dat')
else:
dat_fpath = None
java_conf = {'java_memory': java_memory}
b2gpipe_runner(blast, annot_fpath=annot_fpath,
b2gpipe_bin=blast2go_path, prop_fpath=prop_fpath,
dat_fpath=dat_fpath, java_conf=java_conf,
)
blast.close()
blast2go[input_fpath] = annot_fpath
# prepare pipeline
pipeline = [annotate_gos]
configuration = {}
for input_ in inputs['input']:
input_fpath = input_.last_version
step_config = {'annot_fpath': blast2go[input_fpath]}
configuration[input_.basename] = {'annotate_gos': step_config}
result = self._run_annotation(pipeline=pipeline,
configuration=configuration,
inputs=inputs, output_dir=db_dir)
return result
def test_go_annotator():
'It test the go annotator'
blast = open(os.path.join(TEST_DATA_DIR, 'blastResult.xml'))
prop_fpath = os.path.join(TEST_DATA_DIR, 'b2gPipe.properties')
b2gpipe_bin = os.path.join(guess_jar_dir('blast2go.jar'),
'blast2go.jar')
fhand, annot_fpath = tempfile.mkstemp()
os.close(fhand)
if not b2gpipe_bin:
print "Do not run b2gppe tests, blast2go jar file not found "
return
b2gpipe_runner(blast, annot_fpath, b2gpipe_bin, prop_fpath=prop_fpath)
blast2go = annot_fpath
go_annotator = create_go_annotator(blast2go)
seq = SeqWithQuality(name='seq1', seq=Seq('aaaa'))
go_annotator(seq)
assert 'GO:0009853' in seq.annotations['GOs']
os.remove(annot_fpath)
def test_run_b2g4pipe():
'It test the runner of b2g4pipe'
blast = open(os.path.join(TEST_DATA_DIR, 'blast2.xml'))
fhand, annot_fpath = tempfile.mkstemp()
os.close(fhand)
fhand, dat_fpath = tempfile.mkstemp()
os.close(fhand)
prop_fpath = os.path.join(TEST_DATA_DIR, 'b2gPipe.properties')
b2gpipe_bin = os.path.join(guess_jar_dir('blast2go.jar'),
'blast2go.jar')
if not b2gpipe_bin:
print "Do not run b2gppe tests, blast2go jar file not found "
return
b2gpipe_runner(blast, annot_fpath, b2gpipe_bin, prop_fpath, dat_fpath)
assert os.path.exists(annot_fpath)
assert os.path.exists(dat_fpath)
os.remove(annot_fpath)
os.remove(dat_fpath)