本文整理汇总了Python中qiita_ware.ebi.EBISubmission.add_sample_prep方法的典型用法代码示例。如果您正苦于以下问题：Python EBISubmission.add_sample_prep方法的具体用法？Python EBISubmission.add_sample_prep怎么用？Python EBISubmission.add_sample_prep使用的例子？那么, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类qiita_ware.ebi.EBISubmission的用法示例。
在下文中一共展示了EBISubmission.add_sample_prep方法的10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_add_sample_prep_exception
# 需要导入模块: from qiita_ware.ebi import EBISubmission [as 别名]
# 或者: from qiita_ware.ebi.EBISubmission import add_sample_prep [as 别名]
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2: test_generate_submission_xml
# 需要导入模块: from qiita_ware.ebi import EBISubmission [as 别名]
# 或者: from qiita_ware.ebi.EBISubmission import add_sample_prep [as 别名]
def test_generate_submission_xml(self):
submission = EBISubmission('001', 'teststudy', 'test asbstract',
'metagenome')
submission.add_sample('test1')
submission.add_sample_prep('test1', 'ILLUMINA', 'fastq',
'__init__.py', 'experiment description',
'library protocol')
with self.assertRaises(NoXMLError):
submission.generate_submission_xml('VALIDATE')示例3: test_write_experiment_xml
# 需要导入模块: from qiita_ware.ebi import EBISubmission [as 别名]
# 或者: from qiita_ware.ebi.EBISubmission import add_sample_prep [as 别名]
def test_write_experiment_xml(self):
submission = EBISubmission('001', 'teststudy', 'test asbstract',
'metagenome')
submission.add_sample('test1')
submission.add_sample_prep('test1', 'ILLUMINA', 'fastq',
'fakepath', 'experiment description',
'library protocol')
fh, output = mkstemp()
close(fh)
submission.write_experiment_xml(output)
obs_stripped = ''.join([l.strip() for l in open(output)])
exp_stripped = ''.join([l.strip() for l in EXPERIMENTXML.splitlines()])
self.assertEqual(obs_stripped, exp_stripped)
remove(output)示例4: test_generate_run_xml
# 需要导入模块: from qiita_ware.ebi import EBISubmission [as 别名]
# 或者: from qiita_ware.ebi.EBISubmission import add_sample_prep [as 别名]
def test_generate_run_xml(self):
submission = EBISubmission('001', 'teststudy', 'test asbstract',
'metagenome')
submission.add_sample('test1')
submission.add_sample_prep('test1', 'ILLUMINA', 'fastq',
join(self.path, '__init__.py'),
'experiment description',
'library protocol')
xmlelement = submission.generate_run_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 RUNXML.splitlines()])
self.assertEqual(obs_stripped, exp_stripped)示例5: test_add_sample_prep
# 需要导入模块: from qiita_ware.ebi import EBISubmission [as 别名]
# 或者: from qiita_ware.ebi.EBISubmission import add_sample_prep [as 别名]
def test_add_sample_prep(self):
submission = EBISubmission('001', 'teststudy', 'test asbstract',
'metagenome')
submission.add_sample('test1')
submission.add_sample('test2')
submission.add_sample_prep('test1', 'ILLUMINA', 'fastq',
self.path, 'experiment description',
'library protocol')
prep_info = submission.samples['test1']['preps'][0]
self.assertEqual(prep_info['platform'], 'ILLUMINA')
self.assertEqual(prep_info['file_path'], self.path)
with self.assertRaises(KeyError):
submission.add_sample_prep('test3', 'ILLUMINA', 'fastq',
self.path, 'experiment description',
'library protocol')示例6: test_add_sample_prep_exception
# 需要导入模块: from qiita_ware.ebi import EBISubmission [as 别名]
# 或者: from qiita_ware.ebi.EBISubmission import add_sample_prep [as 别名]
def test_add_sample_prep_exception(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', 'desc1')
with self.assertRaises(ValueError):
submission.add_sample_prep('test2', 'DOES-NOT-EXIST', 'fastq',
self.sample1_fp,
'experiment description',
'library protocol')
with self.assertRaises(KeyError):
submission.add_sample_prep('test3', 'DOES-NOT-EXIST', 'fastq',
self.sample3_fp,
'experiment description',
'library protocol')示例7: test_write_experiment_xml
# 需要导入模块: from qiita_ware.ebi import EBISubmission [as 别名]
# 或者: from qiita_ware.ebi.EBISubmission import add_sample_prep [as 别名]
def test_write_experiment_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_prep('test1', 'ILLUMINA', 'fastq',
self.sample1_fp, 'experiment description',
'library protocol')
fh, output = mkstemp()
close(fh)
submission.write_experiment_xml(output)
obs_stripped = ''.join([l.strip() for l in open(output)])
exp = EXPERIMENTXML % {
'path': self.sample1_fp,
'organization_prefix': qiita_config.ebi_organization_prefix}
exp_stripped = ''.join([l.strip() for l in exp.splitlines()])
self.assertEqual(obs_stripped, exp_stripped)
remove(output)示例8: test_generate_experiment_xml
# 需要导入模块: from qiita_ware.ebi import EBISubmission [as 别名]
# 或者: from qiita_ware.ebi.EBISubmission import add_sample_prep [as 别名]
def test_generate_experiment_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_prep('test1', 'ILLUMINA', 'fastq',
self.sample1_fp,
'experiment description',
'library protocol')
xmlelement = submission.generate_experiment_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 = EXPERIMENTXML % {
'path': self.sample1_fp,
'organization_prefix': qiita_config.ebi_organization_prefix}
exp_stripped = ''.join([l.strip() for l in exp.splitlines()])
self.assertEqual(obs_stripped, exp_stripped)示例9: test_add_sample_prep
# 需要导入模块: from qiita_ware.ebi import EBISubmission [as 别名]
# 或者: from qiita_ware.ebi.EBISubmission import add_sample_prep [as 别名]
def test_add_sample_prep(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', 'desc1')
submission.add_sample_prep('test1', 'ILLUMINA', 'fastq',
self.sample1_fp, 'experiment description',
'library protocol')
prep_info = submission.samples['test1']['prep']
self.assertEqual(prep_info['platform'], 'ILLUMINA')
self.assertEqual(prep_info['file_path'], self.sample1_fp)
with self.assertRaises(KeyError):
submission.add_sample_prep('test3', 'ILLUMINA', 'fastq',
self.sample3_fp,
'experiment description',
'library protocol')示例10: test_generate_run_xml
# 需要导入模块: from qiita_ware.ebi import EBISubmission [as 别名]
# 或者: from qiita_ware.ebi.EBISubmission import add_sample_prep [as 别名]
def test_generate_run_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_prep('test1', 'ILLUMINA', 'fastq',
self.sample1_fp,
'experiment description',
'library protocol')
xmlelement = submission.generate_run_xml()
xml = minidom.parseString(ET.tostring(xmlelement))
# insert the proper EBI directory, since it is a timestamp and hard
# to predict
RUNXML_mod = RUNXML % {
'study_alias': submission._get_study_alias(),
'ebi_dir': submission.ebi_dir,
'organization_prefix': qiita_config.ebi_organization_prefix}
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 RUNXML_mod.splitlines()])
self.assertEqual(obs_stripped, exp_stripped)