本文整理汇总了Python中Client.Client.translateAll方法的典型用法代码示例。如果您正苦于以下问题：Python Client.translateAll方法的具体用法？Python Client.translateAll怎么用？Python Client.translateAll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Client.Client的用法示例。
在下文中一共展示了Client.translateAll方法的1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: __init__
# 需要导入模块: from Client import Client [as 别名]
# 或者: from Client.Client import translateAll [as 别名]
class ext:
"""
These are some helper extensions pretty specific to
what I have been working on.
May be useful to someone else? Maybe not.
"""
def __init__(self, cache_dir='data', base_url="http://babel.gdxbase.org/cgi-bin/translate.cgi"):
self.client = Client(base_url)
self.cache_dir = cache_dir
def mergeProbes(self, idLists):
"""
Returns a list of 2-tuples (i,j) where i is the index in ids1 that matches ids2
"""
#figure out what type of data
idtypes =[self.discoverID(idList, self._getProbeTypes()) for idList in idLists]
for i, idtype in enumerate(idtypes):
if idtype == None:
raise pyBabelError("id " + str(i) + " undefined.")
#get the type map table
typeMap = self.getMap(idtypes)
#build dicts from idname->indx
indxMaps = [self._buildIndexMap(idList) for idList in idLists]
#we only want unique mappings
merged = {}
for row in typeMap:
entrez = row[-1]
if entrez != None:
good = True
for i, column in enumerate(row[:-1]):
if column not in indxMaps[i]:
good = False
if good:
merged[tuple(row[:-1])] = 1
return merged.keys()
def getControls(self, ids):
"""
returns a list of indices that are controls
#have no gene entrez_id
"""
pass #no idea if this is working or not.
idtype = self.discoverID(ids, self._getProbeTypes())
if idtype == None:
raise pyBabelError("ids undefined")
map = self.getAllTable(idtype, idtype)
#print self.prettyPrint(map)
indxMap = self._buildIndexMap(ids)
res = []
for i, _ , entrez in map:
if entrez == None and i in indxMap:
res.append(i)
return res
def discoverID(self, ids, base_idTypes, numIDs=10):
"""
Given a subset of base_idTypes check which
id type a set of ids come from
"""
for idtype in base_idTypes:
if len(self.client.translate(input_type=idtype, input_ids=ids[:numIDs],output_types=[idtype]) ) > 0:
return idtype
return None
def getAllTable(self, idtypes):
input_type = idtypes[0]
output_type = idtypes[1:]
output_type.append('gene_entrez') #for control filtering
return self.client.translateAll(input_type=input_type, output_types=output_type)
def _getProbeTypes(self):
"""
returns a list of valid idtypes that have the word 'probe' in them
"""
p = re.compile('probe')
return [x for x in self.client.getIDTypes() if p.search(x)]
def prettyPrint(self, table):
"""
Little helper function that takes a table and returns a print friendly
string.
"""
return '\n'.join(['\t'.join([str(val) for val in row]) for row in table])
def getMap(self, idtypes, usePickle=True):
"""
"""
#look for pickle
if usePickle:
p = self._getPickle(idtypes)
else:
p = None
if p == None:#not kosher
map = self.getAllTable(idtypes)
#.........这里部分代码省略.........