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？那么恭喜您, 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20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，您的评价将有助于我们的系统推荐出更棒的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)
开发者ID:MarkBruns，项目名称:qiita，代码行数:7，代码来源:test_ebi.py
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)
开发者ID:MarkBruns，项目名称:qiita，代码行数:7，代码来源:test_ebi.py
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)
开发者ID:MarkBruns，项目名称:qiita，代码行数:7，代码来源:test_ebi.py
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)
开发者ID:Jorge-C，项目名称:qiita，代码行数:8，代码来源:test_ebi.py
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)
开发者ID:Jorge-C，项目名称:qiita，代码行数:8，代码来源:test_ebi.py
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)
开发者ID:Jorge-C，项目名称:qiita，代码行数:8，代码来源:test_ebi.py
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')
开发者ID:Jorge-C，项目名称:qiita，代码行数:9，代码来源:test_ebi.py
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')
开发者ID:Jorge-C，项目名称:qiita，代码行数:9，代码来源:test_ebi.py
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)
开发者ID:Jorge-C，项目名称:qiita，代码行数:9，代码来源:test_ebi.py
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')
开发者ID:Jorge-C，项目名称:qiita，代码行数:9，代码来源:test_ebi.py
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')
开发者ID:Jorge-C，项目名称:qiita，代码行数:9，代码来源:test_ebi.py
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')
开发者ID:MarkBruns，项目名称:qiita，代码行数:10，代码来源:test_ebi.py
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)
开发者ID:Jorge-C，项目名称:qiita，代码行数:11，代码来源:test_ebi.py
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)
开发者ID:MarkBruns，项目名称:qiita，代码行数:12，代码来源:test_ebi.py
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)
开发者ID:MarkBruns，项目名称:qiita，代码行数:14，代码来源:test_ebi.py
示例16: test_add_samples_from_templates
def test_add_samples_from_templates(self):
sample_template = StringIO(EXP_SAMPLE_TEMPLATE)
prep_template = StringIO(EXP_PREP_TEMPLATE)
submission = EBISubmission('001', 'teststudy', 'test asbstract',
'metagenome')
submission.add_samples_from_templates(sample_template, prep_template,
self.path)
self.assertTrue('sample1' in submission.samples)
self.assertTrue('sample2' in submission.samples)
self.assertTrue('sample3' in submission.samples)
self.assertEqual(submission.samples['sample2']['preps'][0]['platform'],
'ILLUMINA')
self.assertEqual(
submission.samples['sample2']['preps'][0]['file_path'],
self.path + '/sample2.fastq.gz')
with self.assertRaises(KeyError):
submission.samples['nothere']
开发者ID:Jorge-C，项目名称:qiita，代码行数:17，代码来源:test_ebi.py
示例17: test_add_samples_from_templates_filter_samples
def test_add_samples_from_templates_filter_samples(self):
sample_template = StringIO(EXP_SAMPLE_TEMPLATE)
prep_template = StringIO(EXP_PREP_TEMPLATE_FILTERED)
submission = EBISubmission('001', 'teststudy', 'test asbstract',
investigation_type='Other',
new_investigation_type='metagenome')
submission.add_samples_from_templates(sample_template, prep_template,
self.path)
self.assertTrue('sample1' in submission.samples)
self.assertTrue('sample2' in submission.samples)
self.assertFalse('sample3' in submission.samples)
self.assertEqual(submission.samples['sample2']['prep']['platform'],
'ILLUMINA')
self.assertEqual(
submission.samples['sample2']['prep']['file_path'],
self.sample2_fp)
with self.assertRaises(KeyError):
submission.samples['nothere']
开发者ID:MarkBruns，项目名称:qiita，代码行数:18，代码来源:test_ebi.py
示例18: test_generate_submission_xml
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')
开发者ID:Jorge-C，项目名称:qiita，代码行数:9，代码来源:test_ebi.py
示例19: submit_EBI_from_files
def submit_EBI_from_files(study_id, sample_template, prep_template,
fastq_dir_fp, output_dir_fp, investigation_type,
action, send):
"""EBI submission from files
Parameters
----------
study_id : int
The study id
sample_template : File
The file handler of the sample template file
prep_template : File
The file handler of the prep template file
fastq_dir_fp : str
The fastq filepath
output_dir_fp : str
The output directory
investigation_type : str
The investigation type string
action : str
The action to perform with this data, valid options are: %s
send : bool
True to actually send the files
"""
study = Study(study_id)
study_id_str = str(study_id)
# Get study-specific output directory and set filepaths
get_output_fp = partial(join, output_dir_fp)
study_fp = get_output_fp('study.xml')
sample_fp = get_output_fp('sample.xml')
experiment_fp = get_output_fp('experiment.xml')
run_fp = get_output_fp('run.xml')
submission_fp = get_output_fp('submission.xml')
if not isdir(output_dir_fp):
makedirs(output_dir_fp)
else:
raise ValueError('The output folder already exists: %s' %
output_dir_fp)
submission = EBISubmission.from_templates_and_per_sample_fastqs(
study_id_str, study.title, study.info['study_abstract'],
investigation_type, sample_template, prep_template,
fastq_dir_fp)
submission.write_all_xml_files(study_fp, sample_fp, experiment_fp, run_fp,
submission_fp, action)
if send:
submission.send_sequences()
submission.send_xml()
开发者ID:Jorge-C，项目名称:qiita，代码行数:53，代码来源:commands.py
示例20: test_generate_curl_command
def test_generate_curl_command(self):
sample_template = StringIO(EXP_SAMPLE_TEMPLATE)
prep_template = StringIO(EXP_PREP_TEMPLATE)
submission = EBISubmission.from_templates_and_per_sample_fastqs(
'001', 'test study', 'abstract',
'type', sample_template, prep_template, self.path)
# Set these artificially since the function depends only on these fps
submission.submission_xml_fp = 'submission.xml'
submission.experiment_xml_fp = 'experiment.xml'
submission.study_xml_fp = 'study.xml'
submission.sample_xml_fp = 'sample.xml'
# this should fail since we have not yet set the run.xml fp
with self.assertRaises(NoXMLError):
submission.generate_curl_command('1', '2', '3', '4')
submission.run_xml_fp = 'run.xml'
test_ebi_seq_xfer_user = 'ebi_seq_xfer_user'
test_ebi_access_key = 'ebi_access_key'
test_ebi_dropbox_url = 'ebi_dropbox_url'
# Without curl certificate authentication
test_ebi_skip_curl_cert = True
obs = submission.generate_curl_command(test_ebi_seq_xfer_user,
test_ebi_access_key,
test_ebi_skip_curl_cert,
test_ebi_dropbox_url)
exp_skip_cert = ('curl -k '
'-F "[email protected]" '
'-F "[email protected]" '
'-F "[email protected]" '
'-F "[email protected]" '
'-F "[email protected]" '
'"ebi_dropbox_url/?auth=ERA%20ebi_seq_xfer_user'
'%20ebi_access_key%3D"')
self.assertEqual(obs, exp_skip_cert)
# With curl certificate authentication
test_ebi_skip_curl_cert = False
obs = submission.generate_curl_command(test_ebi_seq_xfer_user,
test_ebi_access_key,
test_ebi_skip_curl_cert,
test_ebi_dropbox_url)
exp_with_cert = ('curl '
'-F "[email protected]" '
'-F "[email protected]" '
'-F "[email protected]" '
'-F "[email protected]" '
'-F "[email protected]" '
'"ebi_dropbox_url/?auth=ERA%20ebi_seq_xfer_user'
'%20ebi_access_key%3D"')
self.assertEqual(obs, exp_with_cert)
开发者ID:Jorge-C，项目名称:qiita，代码行数:52，代码来源:test_ebi.py
注：本文中的qiita_ware.ebi.EBISubmission类示例由纯净天空整理自Github/MSDocs等源码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。 |
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