def _cvt(pli):
_d = list2dict(pli, 2)
_d = value_convert(_d, _inner_cvt)
for p_source in _d:
if isinstance(_d[p_source], list):
_d[p_source].sort(key=lambda e: e["id"])
return {'pathway': _d}
def load_broadinstitute_exac(data_folder):
t0 = time.time()
exacs = load_broadinstitute_exac_all(data_folder)
for k,v in load_broadinstitute_exac_nontcga(data_folder).items():
try:
exacs[k]["exac"]["nontcga"] = v["exac"]["nontcga"]
except KeyError:
exacs[k] = v
for k,v in load_broadinstitute_exac_nonpsych(data_folder).items():
try:
exacs[k]["exac"]["nonpsych"] = v["exac"]["nonpsych"]
except KeyError:
exacs[k] = v
logging.info("Convert transcript ID to EntrezID")
from ..ensembl.parser import EnsemblParser
from biothings.utils.hub_db import get_src_dump
ensembl_doc = get_src_dump().find_one({"_id":"ensembl"}) or {}
ensembl_dir = ensembl_doc.get("data_folder")
assert ensembl_dir, "Can't find Ensembl data directory (used for id conversion)"
ensembl_parser = EnsemblParser(ensembl_dir)
ensembl_parser._load_ensembl2entrez_li()
ensembl2entrez = list2dict(ensembl_parser.ensembl2entrez_li, 0, alwayslist=True)
for line in tabfile_feeder(os.path.join(ensembl_dir,"gene_ensembl__translation__main.txt")):
_,ensid,transid,_ = line
if transid in exacs:
data = exacs.pop(transid) # pop so no-match means no data in the end
for entrezid in ensembl2entrez.get(ensid,[ensid]):
exacs[entrezid] = data
return exacs
def convert2entrez(self, ensembl2x):
'''convert a dict with ensembl gene ids as the keys to matching entrezgene ids as the keys.'''
if not self.ensembl2entrez_li:
self._load_ensembl2entrez_li()
if not self.ensembl_main:
self.ensembl_main = self.load_ensembl_main()
ensembl2entrez = list2dict(self.ensembl2entrez_li, 0)
entrez2ensembl = list2dict(self.ensembl2entrez_li, 1)
# Now make a dictionary indexed by entrez gene id
print('# of ensembl IDs in total: %d' %
len(set(ensembl2x) | set(ensembl2entrez)))
print('# of ensembl IDs match entrez Gene IDs: %d' %
len(set(ensembl2x) & set(ensembl2entrez)))
print('# of ensembl IDs DO NOT match entrez Gene IDs: %d' %
len(set(ensembl2x) - set(ensembl2entrez)))
# all genes with matched entrez
def _fn(eid, taxid=None):
# need to make a copy of the value here.
d = copy.copy(ensembl2x.get(eid, {}))
# otherwise, it will cause issue when multiple entrezgene ids
return d
# match the same ensembl gene, for example,
# ENSMUSG00000027104 --> (11909, 100047997)
data = value_convert(entrez2ensembl, _fn)
# add those has no matched entrez geneid, using ensembl id as the key
for eid in (set(ensembl2x) - set(ensembl2entrez)):
_g = ensembl2x[eid]
#_g.update(self.ensembl_main.get(eid, {}))
data[eid] = _g
for id in data:
if isinstance(data[id], dict):
_doc = dict_nodup(data[id], sort=True)
else:
# if one entrez gene matches multiple ensembl genes
_doc = dict_attrmerge(data[id], removedup=True, sort=True)
data[id] = _doc
return data
def __init__(self, src_name, data_folder, load_ensembl2entrez=True):
self.data_folder = data_folder
self.ensembl2entrez_li = None
self.ensembl_main = None
if load_ensembl2entrez:
self._load_ensembl2entrez_li(src_name)
self.ensembl2entrez = list2dict(self.ensembl2entrez_li,
0,
alwayslist=True)
def transform(xli2):
gene2uniprot = list2dict(list_nondup(xli2), 2, alwayslist=True)
gene2uniprot = value_convert(gene2uniprot,
_dict_convert,
traverse_list=False)
gid, uniprot = list(gene2uniprot.items())[0]
docs = []
for gid, uniprot in gene2uniprot.items():
doc = {"_id": gid}
doc.update(uniprot)
docs.append(doc)
return docs
def _dict_convert(uniprot_li):
'''
convert [(u'E7ESI2', 'TrEMBL'), (u'P24941', 'Swiss-Prot'),
(u'G3V5T9', 'TrEMBL'), (u'G3V317', 'TrEMBL')] into
{'Swiss-Prot': u'P24941',
'TrEMBL': [u'E7ESI2', u'G3V5T9', u'G3V317']}
'''
_dict = list2dict(uniprot_li, 1)
for k, v in _dict.items():
if isinstance(v, list):
_dict[k] = sorted(v)
return {'uniprot': _dict}
def load_cpdb(data_folder, pathways):
# only import pathways from these sources
PATHWAY_SOURCES_INCLUDED = pathways
VALID_COLUMN_NO = 4
t0 = time.time()
DATA_FILES = []
DATA_FILES.append(os.path.join(data_folder, 'CPDB_pathways_genes_mouse.tab'))
DATA_FILES.append(os.path.join(data_folder, 'CPDB_pathways_genes_yeast.tab'))
DATA_FILES.append(os.path.join(data_folder, 'CPDB_pathways_genes_human.tab'))
_out = []
for DATA_FILE in DATA_FILES:
for ld in tabfile_feeder(DATA_FILE, header=1, assert_column_no=VALID_COLUMN_NO):
p_name, p_id, p_source = ld[:3]
p_source = p_source.lower()
if p_source == 'kegg' and p_id.startswith('path:'):
p_id = p_id[5:]
if p_source in PATHWAY_SOURCES_INCLUDED:
genes = ld[-1].split(",")
for gene in genes:
_out.append((gene, p_name, p_id, p_source))
_out = list2dict(_out, 0, alwayslist=True)
def _inner_cvt(p):
p_name, p_id = p
_d = {'name': p_name}
if p_id != 'None':
_d['id'] = p_id
return _d
def _cvt(pli):
_d = list2dict(pli, 2)
_d = value_convert(_d, _inner_cvt)
for p_source in _d:
if isinstance(_d[p_source], list):
_d[p_source].sort(key=lambda e: e["id"])
return {'pathway': _d}
_out = dict_convert(_out, valuefn=_cvt)
return _out
def src_clean_archives(keep_last=1, src=None, verbose=True, noconfirm=False):
'''clean up archive collections in src db, only keep last <kepp_last>
number of archive.
'''
from biothings.utils.dataload import list2dict
from biothings.utils.common import ask
src = src or get_src_db()
archive_li = sorted([(coll.split('_archive_')[0], coll)
for coll in src.collection_names()
if coll.find('archive') != -1])
archive_d = list2dict(archive_li, 0, alwayslist=1)
coll_to_remove = []
for k, v in archive_d.items():
print(k, end='')
#check current collection exists
if src[k].count() > 0:
cnt = 0
for coll in sorted(v)[:-keep_last]:
coll_to_remove.append(coll)
cnt += 1
print("\t\t%s archived collections marked to remove." % cnt)
else:
print('skipped. Missing current "%s" collection!' % k)
if len(coll_to_remove) > 0:
print("%d archived collections will be removed." % len(coll_to_remove))
if verbose:
for coll in coll_to_remove:
print('\t', coll)
if noconfirm or ask("Continue?") == 'Y':
for coll in coll_to_remove:
src[coll].drop()
print("Done.[%s collections removed]" % len(coll_to_remove))
else:
print("Aborted.")
else:
print("Nothing needs to be removed.")