本文整理汇总了Python中qiita_ware.ebi.EBISubmission类的典型用法代码示例。如果您正苦于以下问题：Python EBISubmission类的具体用法？Python EBISubmission怎么用？Python EBISubmission使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了EBISubmission类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_get_experiment_alias
def test_get_experiment_alias(self):
e = EBISubmission('2', 'Study Title', 'Study Abstract',
investigation_type='Other',
new_investigation_type='metagenome')
e.add_sample('foo', '9606', 'homo sapiens', 'desc1')
exp = '%s_ppdid_2:foo' % qiita_config.ebi_organization_prefix
self.assertEqual(e._get_experiment_alias('foo'), exp)示例2: test_get_library_name
def test_get_library_name(self):
e = EBISubmission('2', 'Study Title', 'Study Abstract',
investigation_type='Other',
new_investigation_type='metagenome')
obs = e._get_library_name("nasty<business>")
exp = "nasty<business>"
self.assertEqual(obs, exp)示例3: test_get_submission_alias
def test_get_submission_alias(self):
e = EBISubmission('2', 'Study Title', 'Study Abstract',
investigation_type='Other',
new_investigation_type='metagenome')
obs = e._get_submission_alias()
exp = '%s_submission_2' % qiita_config.ebi_organization_prefix
self.assertEqual(obs, exp)示例4: test_add_dict_as_tags_and_values
def test_add_dict_as_tags_and_values(self):
e = EBISubmission('2', 'Study Title', 'Study Abstract', 'metagenome')
elm = ET.Element('TESTING', {'foo': 'bar'})
e._add_dict_as_tags_and_values(elm, 'foo', {'x': 'y', '>x': '<y'})
obs = ET.tostring(elm)
exp = ''.join([v.strip() for v in ADDDICTTEST.splitlines()])
self.assertEqual(obs, exp)示例5: test_generate_spot_descriptor
def test_generate_spot_descriptor(self):
e = EBISubmission('2', 'Study Title', 'Study Abstract', 'metagenome')
elm = ET.Element('design', {'foo': 'bar'})
e._generate_spot_descriptor(elm, 'LS454')
exp = ''.join([l.strip() for l in GENSPOTDESC.splitlines()])
obs = ET.tostring(elm)
self.assertEqual(obs, exp)示例6: test_generate_library_descriptor
def test_generate_library_descriptor(self):
e = EBISubmission('2', 'Study Title', 'Study Abstract', 'metagenome')
elm = ET.Element('design', {'foo': 'bar'})
e._generate_library_descriptor(elm, 'sample', 10, 'libconsprot')
exp = ''.join([l.strip() for l in GENLIBDESC.splitlines()])
obs = ET.tostring(elm)
self.assertEqual(obs, exp)示例7: test_add_samples_from_templates_bad_directory
def test_add_samples_from_templates_bad_directory(self):
sample_template = StringIO(EXP_SAMPLE_TEMPLATE)
prep_template = StringIO(EXP_PREP_TEMPLATE)
submission = EBISubmission('001', 'teststudy', 'test asbstract',
'metagenome')
with self.assertRaises(IOError):
submission.add_samples_from_templates(
sample_template, [prep_template],
self.path+'WILL-NOT-EXIST-BOOM')示例8: test__write_xml_file
def test__write_xml_file(self):
e = EBISubmission('2', 'Study Title', 'Study Abstract', 'metagenome')
elm = ET.Element('TESTING', {'foo': 'bar'})
e._write_xml_file(lambda: elm, 'thing', 'testfile')
self.assertEqual(e.thing, 'testfile')
obs = open('testfile').read()
exp = '<?xml version="1.0" encoding="UTF-8"?>\n<TESTING foo="bar"/>\n'
self.assertEqual(obs, exp)
remove('testfile')示例9: test_generate_study_xml
def test_generate_study_xml(self):
submission = EBISubmission('001', 'teststudy', 'test asbstract',
'metagenome')
xmlelement = submission.generate_study_xml()
xml = minidom.parseString(ET.tostring(xmlelement))
xmlstring = xml.toprettyxml(indent=' ', encoding='UTF-8')
obs_stripped = ''.join([l.strip() for l in xmlstring.splitlines()])
exp_stripped = ''.join([l.strip() for l in STUDYXML.splitlines()])
self.assertEqual(obs_stripped, exp_stripped)示例10: test_add_sample_prep_exception
def test_add_sample_prep_exception(self):
submission = EBISubmission('001', 'teststudy', 'test asbstract',
'metagenome')
submission.add_sample('test1')
submission.add_sample('test2')
with self.assertRaises(ValueError):
submission.add_sample_prep('test3', 'DOES-NOT-EXIST', 'fastq',
self.path, 'experiment description',
'library protocol')示例11: test_add_sample
def test_add_sample(self):
submission = EBISubmission('001', 'teststudy', 'test asbstract',
'metagenome')
submission.add_sample('test1')
submission.add_sample('test2')
samples = submission.samples
self.assertTrue('test1' in samples and 'test2' in samples)
with self.assertRaises(SampleAlreadyExistsError):
submission.add_sample('test1')示例12: test_add_sample
def test_add_sample(self):
submission = EBISubmission('001', 'teststudy', 'test asbstract',
investigation_type='Other',
new_investigation_type='metagenome')
submission.add_sample('test1', '9606', 'homo sapiens', 'desc1')
submission.add_sample('test2', '9606', 'homo sapiens', 'desc2')
samples = submission.samples
self.assertTrue('test1' in samples and 'test2' in samples)
with self.assertRaises(SampleAlreadyExistsError):
submission.add_sample('test1', '9606', 'homo sapiens', 'desc1')示例13: test_write_study_xml
def test_write_study_xml(self):
submission = EBISubmission('001', 'teststudy', 'test asbstract',
'metagenome')
fh, output = mkstemp()
submission.write_study_xml(output)
close(fh)
obs_stripped = ''.join([l.strip() for l in open(output)])
exp_stripped = ''.join([l.strip() for l in STUDYXML.splitlines()])
self.assertEqual(obs_stripped, exp_stripped)
remove(output)示例14: test_generate_sample_xml
def test_generate_sample_xml(self):
submission = EBISubmission('001', 'teststudy', 'test asbstract',
investigation_type='Other',
new_investigation_type='metagenome')
submission.add_sample('test1', '9606', 'homo sapiens', 'desc1')
submission.add_sample('test2', '9606', 'homo sapiens', 'desc2')
xmlelement = submission.generate_sample_xml()
xml = minidom.parseString(ET.tostring(xmlelement))
xmlstring = xml.toprettyxml(indent=' ', encoding='UTF-8')
obs_stripped = ''.join([l.strip() for l in xmlstring.splitlines()])
exp_stripped = ''.join([l.strip() for l in SAMPLEXML.splitlines()])
self.assertEqual(obs_stripped, exp_stripped)示例15: test_write_sample_xml
def test_write_sample_xml(self):
submission = EBISubmission('001', 'teststudy', 'test asbstract',
investigation_type='Other',
new_investigation_type='metagenome')
submission.add_sample('test1', '9606', 'homo sapiens', 'desc1')
submission.add_sample('test2', '9606', 'homo sapiens', 'desc2')
fh, output = mkstemp()
close(fh)
submission.write_sample_xml(output)
obs_stripped = ''.join([l.strip() for l in open(output)])
exp_stripped = ''.join([l.strip() for l in SAMPLEXML.splitlines()])
self.assertEqual(obs_stripped, exp_stripped)
remove(output)