本文整理汇总了Python中status.Status.log方法的典型用法代码示例。如果您正苦于以下问题：Python Status.log方法的具体用法？Python Status.log怎么用？Python Status.log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status.Status的用法示例。
在下文中一共展示了Status.log方法的4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: join_go_terms_with_genes
# 需要导入模块: from status import Status [as 别名]
# 或者: from status.Status import log [as 别名]
def join_go_terms_with_genes():
client = pymongo.MongoClient()
terms = client.go.terms.find()
status = Status('joining terms with genes').n(terms.count())
for k, term in enumerate(terms):
status.log(k)
genes = client.go.genes.find({'go': term['go']})
term['genes'] = list(set(g['gene'] for g in genes))
term['n_genes'] = len(term['genes'])
client.go.terms.save(term)
status.stop()示例2: load_go_terms
# 需要导入模块: from status import Status [as 别名]
# 或者: from status.Status import log [as 别名]
def load_go_terms():
info = {
'database': 'go',
'collection': 'terms',
'url': 'http://geneontology.org/ontology/go.obo',
'timestamp': time.time()
}
client = pymongo.MongoClient()
collection = client[info['database']][info['collection']]
collection.drop()
with mktemp() as pathname:
filename = os.path.join(pathname, 'go.obo')
log.debug('downloading %s to %s', info['url'], filename)
subprocess.call(['wget', info['url'], '-O', filename])
with open(filename, 'rt') as fid:
status = Status(filename, log).fid(fid).start()
obj = None
state = None
for line in fid:
status.log()
line = line.strip()
if line and not line.startswith('!'):
if line[0] == '[' and line[-1] == ']':
if state == 'Term' and obj:
collection.insert(obj)
state = line[1:-1]
obj = {}
elif state == 'Term':
key, _, value = line.partition(': ')
if value:
if key == 'id':
obj['go'] = value
else:
try:
obj[key].append(value)
except KeyError:
obj[key] = value
except AttributeError:
obj[key] = [obj[key], value]
status.stop()
if state == 'Term' and obj:
collection.insert(obj)
collection.create_index('go')
update_info(info)示例3: parse_edges
# 需要导入模块: from status import Status [as 别名]
# 或者: from status.Status import log [as 别名]
def parse_edges(dir, meta_id, id_to_symbol, id_to_ensembl, threshold):
for filename in glob.glob(os.path.join(dir, '*.cor')):
with open(filename) as fid:
status = Status('processing ' + filename, logger=log).fid(fid).start()
for line in fid:
status.log()
try:
source, target, correlation, pvalue = line.split()
correlation = float(correlation)
except Exception as e:
log.error(e.message)
continue
if math.fabs(correlation) > threshold:
try:
yield {'source': id_to_ensembl[source], 'target': id_to_ensembl[target], 'correlation': correlation, 'pvalue': float(pvalue), 'meta': meta_id}
except KeyError as e:
log.error('could not map identifier %s (%s)', e.message, id_to_symbol.get(e.message))
status.stop()示例4: load_go_genes
# 需要导入模块: from status import Status [as 别名]
# 或者: from status.Status import log [as 别名]
def load_go_genes():
info = {
'database': 'go',
'collection': 'genes',
'url': 'http://geneontology.org/gene-associations/gene_association.goa_human.gz',
'timestamp': time.time()
}
client = pymongo.MongoClient()
collection = client[info['database']][info['collection']]
collection.drop()
with mktemp() as pathname:
filename = os.path.join(pathname, 'gene_association.goa_human.gz')
log.debug('downloading %s to %s', info['url'], filename)
subprocess.call(['wget', info['url'], '-O', filename])
log.debug('gunzip %s', filename)
subprocess.call(['gunzip', filename])
filename, _ = os.path.splitext(filename)
with open(filename, 'rt') as fid:
log.debug('creating a name to emsembl id lookup table from go genes...')
go_genes = set([line.split('\t')[2] for line in fid if not line.startswith('!')])
name_to_id = genemania.id_lookup_table(go_genes)
with open(filename, 'rt') as fid:
status = Status(filename, log).fid(fid).start()
for line in fid:
status.log()
if not line.startswith('!'):
tokens = line.split('\t')
obj = {
'gene': name_to_id.get(tokens[2]),
'go': tokens[4]
}
collection.insert(obj)
status.stop()
update_info(info)
collection.create_index('go')
collection.create_index('gene')