def queryUniprot(id, loop_through=[]):
"""Query Uniprot with *id* and return a `dictionary` containing the results
:arg loop_through: entries through which you want to loop dictElements
until there aren't any elements left
:type loop_through: list
"""
if not isinstance(id, str):
raise TypeError('id should be a string')
try:
record_file = openURL(
'http://www.uniprot.org/uniprot/{0}.xml'.format(id))
except:
raise ValueError('No Uniprot record found with that id')
data = record_file.read()
record_file.close()
data = ET.XML(data)
data = dictElement(data.getchildren()[0],
'{http://uniprot.org/uniprot}',
number_multiples=True)
if loop_through != []:
data = dictElementLoop(data, loop_through,
'{http://uniprot.org/uniprot}')
return data
def queryUniprot(id, expand=[], regex=True):
"""Query Uniprot with *id* and return a `dict` containing the raw results.
Regular users should use :func:`searchUniprot` instead.
:arg expand: entries through which you want to loop dictElements
until there aren't any elements left
:type expand: list
"""
if not isinstance(id, str):
raise TypeError('id should be a string')
try:
record_file = openURL(
'http://www.uniprot.org/uniprot/{0}.xml'.format(id))
except:
raise ValueError('No Uniprot record found with that id')
data = record_file.read()
record_file.close()
data = XML(data)
data = dictElement(data.getchildren()[0],
'{http://uniprot.org/uniprot}',
number_multiples=True)
for key in data:
value = data[key]
if not key.startswith('dbReference'):
continue
try:
if value.get('type') != 'PDB':
continue
except AttributeError:
continue
pdbid = value.get('id')
refdata = {'PDB': pdbid}
for prop in value:
prop_key = prop.get('type')
prop_val = prop.get('value')
refdata[prop_key] = prop_val
data[key] = refdata
if expand:
keys = []
if regex:
for lt in expand:
lt_re = re.compile(lt)
for key in data:
if lt_re.match(key):
keys.append(key)
else:
keys = expand
data = dictElementLoop(data, keys, '{http://uniprot.org/uniprot}')
return data
def queryUniprot(id, expand=[], regex=True):
"""Query Uniprot with *id* and return a `dictionary` containing the results
:arg expand: entries through which you want to loop dictElements
until there aren't any elements left
:type expand: list
"""
if not isinstance(id, str):
raise TypeError('id should be a string')
try:
record_file = openURL('http://www.uniprot.org/uniprot/{0}.xml'.format(id))
except:
raise ValueError('No Uniprot record found with that id')
data = record_file.read()
record_file.close()
data = XML(data)
data = dictElement(data.getchildren()[0], '{http://uniprot.org/uniprot}', number_multiples=True)
for key in data:
value = data[key]
if not key.startswith('dbReference'):
continue
try:
if value.get('type') != 'PDB':
continue
except AttributeError:
continue
pdbid = value.get('id')
refdata = {'PDB': pdbid}
for prop in value:
prop_key = prop.get('type')
prop_val = prop.get('value')
refdata[prop_key] = prop_val
data[key] = refdata
if expand:
keys = []
if regex:
for lt in expand:
lt_re = re.compile(lt)
for key in data.keys():
if lt_re.match(key):
keys.append(key)
else:
keys = expand
data = dictElementLoop(data, keys, '{http://uniprot.org/uniprot}')
return data