本文整理汇总了Python中qiita_db.analysis.Analysis._build_mapping_file方法的典型用法代码示例。如果您正苦于以下问题：Python Analysis._build_mapping_file方法的具体用法？Python Analysis._build_mapping_file怎么用？Python Analysis._build_mapping_file使用的例子？那么恭喜您, 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_db.analysis.Analysis的用法示例。
在下文中一共展示了Analysis._build_mapping_file方法的3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: TestAnalysis
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import _build_mapping_file [as 别名]
#.........这里部分代码省略.........
def test_remove_samples_both(self):
self.analysis.remove_samples(proc_data=(1, ),
samples=('1.SKB8.640193', ))
exp = {1: ['1.SKD8.640184', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_samples(self):
self.analysis.remove_samples(samples=('1.SKD8.640184', ))
exp = {1: ['1.SKB8.640193', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_processed_data(self):
self.analysis.remove_samples(proc_data=(1, ))
exp = {}
self.assertEqual(self.analysis.samples, exp)
def test_share(self):
self.analysis.share(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, ["[email protected]",
"[email protected]"])
def test_unshare(self):
self.analysis.unshare(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, [])
def test_get_samples(self):
obs = self.analysis._get_samples()
exp = {1: ['1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192']}
self.assertEqual(obs, exp)
def test_build_mapping_file(self):
new_id = get_count('qiita.filepath') + 1
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_mapping_file(samples)
obs = self.analysis.mapping_file
self.assertEqual(obs, self.map_fp)
base_dir = get_mountpoint('analysis')[0][1]
obs = pd.read_csv(obs, sep='\t', infer_datetime_format=True,
parse_dates=True, index_col=False, comment='\t')
exp = pd.read_csv(join(base_dir, '1_analysis_mapping_exp.txt'),
sep='\t', infer_datetime_format=True,
parse_dates=True, index_col=False, comment='\t')
assert_frame_equal(obs, exp)
sql = """SELECT * FROM qiita.filepath
WHERE filepath=%s ORDER BY filepath_id"""
obs = self.conn_handler.execute_fetchall(
sql, ("%d_analysis_mapping.txt" % self.analysis.id,))
exp = [[13, '1_analysis_mapping.txt', 9, '852952723', 1, 1],
[new_id, '1_analysis_mapping.txt', 9, '1606265094', 1, 1]]
self.assertEqual(obs, exp)
sql = """SELECT * FROM qiita.analysis_filepath
WHERE analysis_id=%s ORDER BY filepath_id"""
obs = self.conn_handler.execute_fetchall(sql, (self.analysis.id,))
exp = [[1L, 14L, 2L], [1L, 15L, None], [1L, new_id, None]]
def test_build_mapping_file_duplicate_samples(self):
samples = {1: ['1.SKB8.640193', '1.SKB8.640193', '1.SKD8.640184']}
with self.assertRaises(QiitaDBError):示例2: TestAnalysis
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import _build_mapping_file [as 别名]
#.........这里部分代码省略.........
def test_remove_samples_both(self):
self.analysis.remove_samples(proc_data=(1, ),
samples=('1.SKB8.640193', ))
exp = {1: ['1.SKD8.640184', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_samples(self):
self.analysis.remove_samples(samples=('1.SKD8.640184', ))
exp = {1: ['1.SKB8.640193', '1.SKB7.640196', '1.SKM9.640192',
'1.SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_processed_data(self):
self.analysis.remove_samples(proc_data=(1, ))
exp = {}
self.assertEqual(self.analysis.samples, exp)
def test_share(self):
self.analysis.share(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, ["[email protected]",
"[email protected]"])
def test_unshare(self):
self.analysis.unshare(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, [])
def test_get_samples(self):
obs = self.analysis._get_samples()
exp = {1: ['1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192']}
self.assertEqual(obs, exp)
def test_build_mapping_file(self):
samples = {1: ['1.SKB8.640193', '1.SKD8.640184', '1.SKB7.640196']}
self.analysis._build_mapping_file(samples,
conn_handler=self.conn_handler)
obs = self.analysis.mapping_file
self.assertEqual(obs, self.map_fp)
with open(self.map_fp) as f:
mapdata = f.readlines()
# check some columns for correctness
obs = [line.split('\t')[0] for line in mapdata]
exp = ['#SampleID', '1.SKB8.640193', '1.SKD8.640184',
'1.SKB7.640196']
self.assertEqual(obs, exp)
obs = [line.split('\t')[1] for line in mapdata]
exp = ['BarcodeSequence', 'AGCGCTCACATC', 'TGAGTGGTCTGT',
'CGGCCTAAGTTC']
self.assertEqual(obs, exp)
obs = [line.split('\t')[2] for line in mapdata]
exp = ['LinkerPrimerSequence', 'GTGCCAGCMGCCGCGGTAA',
'GTGCCAGCMGCCGCGGTAA', 'GTGCCAGCMGCCGCGGTAA']
self.assertEqual(obs, exp)
obs = [line.split('\t')[19] for line in mapdata]
exp = ['host_subject_id', '1001:M7', '1001:D9',
'1001:M8']
self.assertEqual(obs, exp)
obs = [line.split('\t')[47] for line in mapdata]
exp = ['tot_org_carb', '5.0', '4.32', '5.0']
self.assertEqual(obs, exp)示例3: TestAnalysis
# 需要导入模块: from qiita_db.analysis import Analysis [as 别名]
# 或者: from qiita_db.analysis.Analysis import _build_mapping_file [as 别名]
#.........这里部分代码省略.........
self.assertEqual(new.samples, exp)
def test_remove_samples_both(self):
self.analysis.remove_samples(proc_data=(1, ),
samples=('SKB8.640193', ))
exp = {1: ['SKD8.640184', 'SKB7.640196', 'SKM9.640192', 'SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_samples(self):
self.analysis.remove_samples(samples=('SKD8.640184', ))
exp = {1: ['SKB8.640193', 'SKB7.640196', 'SKM9.640192', 'SKM4.640180']}
self.assertEqual(self.analysis.samples, exp)
def test_remove_samples_processed_data(self):
self.analysis.remove_samples(proc_data=(1, ))
exp = {}
self.assertEqual(self.analysis.samples, exp)
def test_share(self):
self.analysis.share(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, ["[email protected]",
"[email protected]"])
def test_unshare(self):
self.analysis.unshare(User("[email protected]"))
self.assertEqual(self.analysis.shared_with, [])
def test_get_samples(self):
obs = self.analysis._get_samples()
exp = {1: ['SKB7.640196', 'SKB8.640193', 'SKD8.640184', 'SKM4.640180',
'SKM9.640192']}
self.assertEqual(obs, exp)
def test_build_mapping_file(self):
map_fp = join(get_db_files_base_dir(), "analysis",
"1_analysis_mapping.txt")
try:
samples = {1: ['SKB8.640193', 'SKD8.640184', 'SKB7.640196']}
self.analysis._build_mapping_file(samples,
conn_handler=self.conn_handler)
obs = self.analysis.mapping_file
self.assertEqual(obs, map_fp)
with open(map_fp) as f:
mapdata = f.readlines()
# check some columns for correctness
obs = [line.split('\t')[0] for line in mapdata]
exp = ['#SampleID', 'SKB8.640193', 'SKD8.640184', 'SKB7.640196']
self.assertEqual(obs, exp)
obs = [line.split('\t')[1] for line in mapdata]
exp = ['BarcodeSequence', 'AGCGCTCACATC', 'TGAGTGGTCTGT',
'CGGCCTAAGTTC']
self.assertEqual(obs, exp)
obs = [line.split('\t')[2] for line in mapdata]
exp = ['LinkerPrimerSequence', 'GTGCCAGCMGCCGCGGTAA',
'GTGCCAGCMGCCGCGGTAA', 'GTGCCAGCMGCCGCGGTAA']
self.assertEqual(obs, exp)
obs = [line.split('\t')[19] for line in mapdata]
exp = ['host_subject_id', '1001:M7', '1001:D9',
'1001:M8']
self.assertEqual(obs, exp)
obs = [line.split('\t')[47] for line in mapdata]