def translate_identifiers():
if 'ids' not in request.forms:
return template('translate',
{
'results': None,
'namespaces': namespace_fullname.items(),
})
inputns = request.forms['inputns']
outputns = request.forms['outputns']
results = []
for i in request.forms['ids'].strip().split():
i = i.strip()
if not len(i):
continue
e = translate(i, inputns, 'ensembl:gene_id')
o = translate(e, 'ensembl:gene_id', outputns)
results.append((i,e,o))
if format == 'csv':
return '\n'.join('\t'.join(r) for r in results)
if format == 'json':
from collections import namedtuple
rtype = namedtuple('WaldoIDTranslation', 'input ensembl_gene output')
results = [rtype(r) for r in results]
return json.dumps(results)
return template('translate',
{ 'results': results,
'inputns_user' : namespace_fullname[inputns],
'outputns_user' : namespace_fullname[outputns],
'namespaces': namespace_fullname.items(),
})
def from_ensembl_peptide_id(ensembl_peptide_id, session=None):
'''
mgi_id = from_ensembl_peptide_id(ensembl_peptide_id, session={backend.create_session()})
Convert ensembl_peptide_id to mgi ID (MGI:00xxxxxx)
Parameters
----------
ensembl_peptide_id : Ensembl peptide ID
session : SQLAlchemy session to use (default: call backend.create_session())
Returns
-------
mgi_id : MGI ID
'''
return translate(ensembl_peptide_id, 'ensembl:peptide_id', 'mgi:id', session)
def from_ensembl_gene_id(ensembl_gene_id, session=None):
'''
locate_id = from_ensembl_gene_id(ensembl_gene_id, session={backend.create_session()})
Convert ensembl_gene_id to LOCATE uid.
Parameters
----------
ensembl_gene_id : Ensembl gene ID
session : SQLAlchemy session to use (default: call backend.create_session())
Returns
-------
locate_id : LOCATE protein identifier
'''
return translate(ensembl_gene_id, 'ensembl:gene_id', 'locate:id', session)
def search(format='html'):
q = request.query.q
rs = session.query(waldo.uniprot.models.Entry).filter_by(rname=q).all()
if len(rs) == 0:
rs = waldo.uniprot.retrieve.retrieve_name_matches(q)
if len(rs) == 1:
(e,) = rs
return _result(format, 'Uniprot', e.name, translate(e.name, 'uniprot:name', 'ensembl:gene_id'))
elif len(rs) == 0:
return template('index', {
'message' : 'No results found.',
})
else:
return template('many', {
'results': rs,
'search_term_value': q,
})
def get_information(protein_id, session=None):
"""
information = get_information(protein_id, session={backend.create_session()})
Returns all information on the protein identified by `protein_id`
Parameters
----------
protein_id : string
protein ID in one of the formats accepted by Waldo
session : database connection, optional
database connection to use
Returns
-------
information : string
CSV representation of all information on `protein_id`
"""
def get_data(module):
spec_id = module.from_ensembl_gene_id(ensemblgene, session)
if not spec_id:
return "None, None"
locs = module.retrieve_go_annotations(spec_id)
all_locs = []
for ls in locs:
all_locs.extend([loc.strip() for loc in re.split("[,.;:]+", ls)])
all_locs = list(set(all_locs))
all_locs = ";".join(all_locs)
url = module.gen_url(spec_id)
return "%s,%s" % (all_locs, url)
if session is None:
session = waldo.backend.create_session()
ensemblgene = translate(protein_id, get_id_namespace(protein_id), "ensembl:gene_id", session)
return ",".join(
[
ensemblgene,
get_data(waldo.uniprot.retrieve),
get_data(waldo.mgi.retrieve),
get_data(waldo.locate.retrieve),
get_data(waldo.hpa.retrieve),
]
)
def from_ensembl_peptide_id(ensembl_peptide_id, session=None):
'''
name = from ensembl_peptide_id(ensembl_peptide_id, session={backend.create_session()})
Convert ensembl_peptide_id to Uniprot name/ID.
Parameters
----------
ensembl_peptide_id : str
Ensembl protein ID
session : SQLAlchemy session
Session to use (default: create a new one)
Returns
-------
name : str
Uniprot peptide name
'''
return translate(ensembl_peptide_id, 'ensembl:peptide_id', 'uniprot:name', session)
def from_ensembl_gene_id(ensembl_gene_id, session=None):
'''
name = from_ensembl_gene_id(ensembl_gene_id, session={backend.create_session()})
Convert ensembl_gene_id to uniprot name (uniprot ID).
Parameters
----------
ensembl_gene_id : str
Ensembl gene ID
session : SQLAlchemy session
Session to use (default: call backend.create_session())
Returns
-------
name : str
uniprot gene name
'''
return translate(ensembl_gene_id, 'ensembl:gene_id', 'uniprot:name', session)
def test_retrieve():
ensembl = 'ENSG00000070785'
uid = '6000005'
engine = create_engine('sqlite://')
metadata = waldo.locate.models.Base.metadata
metadata.bind = engine
metadata.create_all()
sessionmaker_ = sessionmaker(engine)
waldo.locate.load.load(_testdir, sessionmaker_)
session = sessionmaker_()
locid = translate(ensembl, 'ensembl:gene_id', 'locate:id', session)
assert locid == uid
ret = waldo.locate.retrieve.from_ensembl_gene_id(ensembl, session)
assert ret == uid
goids = waldo.locate.retrieve.retrieve_go_annotations(ret, session)
entry = waldo.locate.retrieve.retrieve_entry(locid, session)
assert len(entry.organisms) == 1
def search(format='html'):
locateid = request.query.locateid
return _result(format, 'LOCATE ID', locateid, translate(locateid.upper(), 'locate:id', 'ensembl:gene_id'))
def search(format='html'):
uniprotacc = request.query.uniprotacc
return _result(format, 'Uniprot Accession ID', uniprotacc, translate(uniprotacc.upper(), 'uniprot:accession', 'ensembl:gene_id'))
def search(format='html'):
uniprotname = request.query.uniprotname
return _result(format, 'Uniprot Name', uniprotname, translate(uniprotname.upper(), 'uniprot:name', 'ensembl:gene_id'))
def search(format='html'):
mgiid = request.query.mgiid
if not mgiid.startswith('MGI:'):
mgiid = 'MGI:'+mgiid
return _result(format, 'MGI ID', mgiid, translate(mgiid, 'mgi:id', 'ensembl:gene_id'))
def test_nr_entries():
nr_entries = len(re.findall("ENSMUSG", gzip.GzipFile(_testfile).read()))
session, loaded = _load_refseq_test()
assert loaded == nr_entries
assert translate("NP_112436", "refseq:accession", "ensembl:gene_id", session) == "ENSMUSG00000040613"