def create_ref_sources(self):
# create an entrez ref and ensembl ref (optional)
self.entrez_ref = make_ref_source(self.record['entrezgene']['@source'], PROPS['Entrez Gene ID'],
self.external_ids['Entrez Gene ID'], login=self.login)
if 'Ensembl Gene ID' in self.external_ids:
if len(self.external_ids['Ensembl Gene ID']) != 1:
raise ValueError("more than one ensembl gene ID: {}".format(self.record['entrezgene']))
ensembl_gene_id = list(self.external_ids['Ensembl Gene ID'])[0]
self.ensembl_ref = make_ref_source(self.record['ensembl']['@source'], PROPS['Ensembl Gene ID'],
ensembl_gene_id, login=self.login)
def create_ref_sources(self):
# create an entrez ref and ensembl ref (optional)
self.entrez_ref = make_ref_source(self.record['entrezgene']['@source'], PROPS['Entrez Gene ID'],
self.external_ids['Entrez Gene ID'], login=self.login)
if 'Reference Ensembl Gene ID' in self.external_ids:
self.ensembl_ref = make_ref_source(self.record['ensembl']['@source'], PROPS['Ensembl Gene ID'],
self.external_ids['Reference Ensembl Gene ID'], login=self.login)
elif 'Ensembl Gene ID' in self.external_ids:
if len(self.external_ids['Ensembl Gene ID']) == 1:
self.ensembl_ref = make_ref_source(self.record['ensembl']['@source'], PROPS['Ensembl Gene ID'],
list(self.external_ids['Ensembl Gene ID'])[0], login=self.login)
def create_statements(self):
"""
create statements common to all proteins
"""
s = []
############
# ID statements
# Required: uniprot (1)
# Optional: OMIM (1?), Ensembl protein (0 or more), refseq protein (0 or more)
############
entrez_gene = self.external_ids['Entrez Gene ID']
uniprot_ref = make_ref_source(self.record['uniprot']['@source'], PROPS['UniProt ID'],
self.external_ids['UniProt ID'],
login=self.login)
entrez_ref = make_ref_source(self.record['entrezgene']['@source'], PROPS['Entrez Gene ID'],
self.external_ids['Entrez Gene ID'], login=self.login)
s.append(wdi_core.WDString(self.external_ids['UniProt ID'], PROPS['UniProt ID'], references=[uniprot_ref]))
for key in ['Saccharomyces Genome Database ID']:
if key in self.external_ids:
s.append(wdi_core.WDString(self.external_ids[key], PROPS[key], references=[entrez_ref]))
key = 'Ensembl Protein ID'
if key in self.external_ids:
for id in self.external_ids[key]:
ref = make_ref_source(self.record['ensembl']['@source'], PROPS[key], id, login=self.login)
s.append(wdi_core.WDString(id, PROPS[key], references=[ref]))
key = 'RefSeq Protein ID'
if key in self.external_ids:
for id in self.external_ids[key]:
ref = make_ref_source(self.record['refseq']['@source'], PROPS['Entrez Gene ID'], entrez_gene,
login=self.login)
s.append(wdi_core.WDString(id, PROPS[key], references=[ref]))
############
# Protein statements
############
# instance of protein
s.append(wdi_core.WDItemID("Q8054", PROPS['instance of'], references=[uniprot_ref]))
# found in taxon
s.append(wdi_core.WDItemID(self.organism_info['wdid'], PROPS['found in taxon'], references=[uniprot_ref]))
# encoded by
s.append(wdi_core.WDItemID(self.gene_wdid, PROPS['encoded by'], references=[uniprot_ref]))
return s
def create_gp_statements(self):
"""
Create genomic_pos start stop orientation plus chromosome qualifiers
:return:
"""
genomic_pos_value = self.record['genomic_pos']['@value'][0]
genomic_pos_source = self.record['genomic_pos']['@source']
genomic_pos_id_prop = source_ref_id[genomic_pos_source['id']]
assert isinstance(self.external_ids[genomic_pos_id_prop], str)
external_id = self.external_ids[genomic_pos_id_prop]
genomic_pos_ref = make_ref_source(genomic_pos_source, PROPS[genomic_pos_id_prop], external_id, login=self.login)
s = []
# create qualifier for chromosome (which has the refseq ID on it)
chr_refseq = genomic_pos_value['chr']
chr_qid = self.refseq_qid_chrom[chr_refseq]
qualifiers = [wdi_core.WDItemID(value=chr_qid, prop_nr=PROPS['chromosome'], is_qualifier=True)]
# strand orientation
strand_orientation = 'Q22809680' if genomic_pos_value['strand'] == 1 else 'Q22809711'
s.append(wdi_core.WDItemID(strand_orientation, PROPS['strand orientation'],
references=[genomic_pos_ref], qualifiers=qualifiers))
# genomic start and end
s.append(wdi_core.WDString(str(int(genomic_pos_value['start'])), PROPS['genomic start'],
references=[genomic_pos_ref], qualifiers=qualifiers))
s.append(wdi_core.WDString(str(int(genomic_pos_value['end'])), PROPS['genomic end'],
references=[genomic_pos_ref], qualifiers=qualifiers))
return s
def make_gene_encodes(self, write=True):
"""
Add an "encodes" statement to the gene item
:return:
"""
uniprot_ref = make_ref_source(self.record['uniprot']['@source'], PROPS['UniProt ID'],
self.external_ids['UniProt ID'],
login=self.login)
try:
statements = [wdi_core.WDItemID(self.protein_wdid, PROPS['encodes'], references=[uniprot_ref])]
wd_item_gene = wdi_core.WDItemEngine(wd_item_id=self.gene_wdid,data=statements,
append_value=[PROPS['encodes']], fast_run=fast_run,
fast_run_base_filter={PROPS['Entrez Gene ID']: '',
PROPS['found in taxon']: self.organism_info[
'wdid']},
global_ref_mode="CUSTOM", ref_handler=update_retrieved_if_new,
core_props=core_props)
wdi_helpers.try_write(wd_item_gene, self.external_ids['UniProt ID'], PROPS['UniProt ID'], self.login,
write=write)
except Exception as e:
exc_info = sys.exc_info()
traceback.print_exception(*exc_info)
msg = wdi_helpers.format_msg(self.external_ids['UniProt ID'], PROPS['UniProt ID'], None,
str(e), msg_type=type(e))
wdi_core.WDItemEngine.log("ERROR", msg)
def make_gene_encodes(self, write=True):
"""
Add an "encodes" statement to the gene item
:return:
"""
uniprot_ref = make_ref_source(self.record['uniprot']['@source'],
PROPS['UniProt ID'],
self.external_ids['UniProt ID'],
login=self.login)
try:
statements = [
wdi_core.WDItemID(self.protein_wdid,
PROPS['encodes'],
references=[uniprot_ref])
]
wd_item_gene = wdi_core.WDItemEngine(
wd_item_id=self.gene_wdid,
domain='genes',
data=statements,
append_value=[PROPS['encodes']])
wdi_helpers.try_write(wd_item_gene,
self.external_ids['UniProt ID'],
PROPS['UniProt ID'],
self.login,
write=write)
except Exception as e:
exc_info = sys.exc_info()
traceback.print_exception(*exc_info)
msg = wdi_helpers.format_msg(self.external_ids['UniProt ID'],
PROPS['UniProt ID'],
None,
str(e),
msg_type=type(e))
wdi_core.WDItemEngine.log("ERROR", msg)
def create_gp_statements_chr(self):
"""
Create genomic_pos start stop orientation on a chromosome
:return:
"""
genomic_pos_value = self.record['genomic_pos']['@value']
genomic_pos_source = self.record['genomic_pos']['@source']
genomic_pos_id_prop = source_ref_id[genomic_pos_source['id']]
genomic_pos_ref = make_ref_source(
genomic_pos_source,
PROPS[genomic_pos_id_prop],
self.external_ids[genomic_pos_id_prop],
login=self.login)
# create qualifier for start/stop/orientation
chrom_wdid = self.chr_num_wdid[genomic_pos_value['chr']]
qualifiers = [
wdi_core.WDItemID(chrom_wdid,
PROPS['chromosome'],
is_qualifier=True)
]
s = []
# strand orientation
strand_orientation = 'Q22809680' if genomic_pos_value[
'strand'] == 1 else 'Q22809711'
s.append(
wdi_core.WDItemID(strand_orientation,
PROPS['strand orientation'],
references=[genomic_pos_ref]))
# genomic start and end
s.append(
wdi_core.WDString(str(int(genomic_pos_value['start'])),
PROPS['genomic start'],
references=[genomic_pos_ref],
qualifiers=qualifiers))
s.append(
wdi_core.WDString(str(int(genomic_pos_value['end'])),
PROPS['genomic end'],
references=[genomic_pos_ref],
qualifiers=qualifiers))
# chromosome
s.append(
wdi_core.WDItemID(chrom_wdid,
PROPS['chromosome'],
references=[genomic_pos_ref]))
return s
def create_statements(self):
# create gene statements
s = Gene.create_statements(self)
entrez_ref = make_ref_source(self.record['entrezgene']['@source'], PROPS['Entrez Gene ID'],
self.external_ids['Entrez Gene ID'], login=self.login)
# add on human specific gene statements
for key in ['HGNC ID', 'HGNC Gene Symbol']:
if key in self.external_ids:
s.append(wdi_core.WDString(self.external_ids[key], PROPS[key], references=[entrez_ref]))
# add on gene position statements
if 'genomic_pos' in self.record:
ss = self.do_gp_human()
if ss:
s.extend(ss)
return s
def create_gp_statements(self):
"""
Create genomic_pos start stop orientation no chromosome
:return:
"""
genomic_pos_value = self.record['genomic_pos']['@value']
genomic_pos_source = self.record['genomic_pos']['@source']
genomic_pos_id_prop = source_ref_id[genomic_pos_source['id']]
genomic_pos_ref = make_ref_source(
genomic_pos_source,
PROPS[genomic_pos_id_prop],
self.external_ids[genomic_pos_id_prop],
login=self.login)
s = []
# create qualifier for chromosome REFSEQ ID (not chrom item)
chromosome = genomic_pos_value['chr']
rs_chrom = wdi_core.WDString(value=chromosome,
prop_nr='P2249',
is_qualifier=True)
# strand orientation
strand_orientation = 'Q22809680' if genomic_pos_value[
'strand'] == 1 else 'Q22809711'
s.append(
wdi_core.WDItemID(strand_orientation,
PROPS['strand orientation'],
references=[genomic_pos_ref],
qualifiers=[rs_chrom]))
# genomic start and end
s.append(
wdi_core.WDString(str(int(genomic_pos_value['start'])),
PROPS['genomic start'],
references=[genomic_pos_ref],
qualifiers=[rs_chrom]))
s.append(
wdi_core.WDString(str(int(genomic_pos_value['end'])),
PROPS['genomic end'],
references=[genomic_pos_ref],
qualifiers=[rs_chrom]))
return s
def do_gp_human(self):
"""
create genomic pos, chr, strand statements for human
includes genomic assembly
genes that are on an unlocalized scaffold will have no genomic position statements
example: https://mygene.info/v3/gene/102724770
https://www.wikidata.org/wiki/Q20970159
:return:
"""
genomic_pos_value = self.record['genomic_pos']['@value']
if genomic_pos_value['chr'] not in self.chr_num_wdid:
return []
genomic_pos_source = self.record['genomic_pos']['@source']
genomic_pos_id_prop = source_ref_id[genomic_pos_source['id']]
genomic_pos_ref = make_ref_source(
genomic_pos_source,
PROPS[genomic_pos_id_prop],
self.external_ids[genomic_pos_id_prop],
login=self.login)
assembly = wdi_core.WDItemID("Q20966585",
PROPS['genomic assembly'],
is_qualifier=True)
# create qualifier for start/stop
chrom_wdid = self.chr_num_wdid[genomic_pos_value['chr']]
qualifiers = [
wdi_core.WDItemID(chrom_wdid,
PROPS['chromosome'],
is_qualifier=True), assembly
]
strand_orientation = 'Q22809680' if genomic_pos_value[
'strand'] == 1 else 'Q22809711'
if 'genomic_pos_hg19' in self.record:
do_hg19 = True
genomic_pos_value_hg19 = self.record['genomic_pos_hg19']['@value']
genomic_pos_source_hg19 = self.record['genomic_pos_hg19'][
'@source']
genomic_pos_id_prop_hg19 = source_ref_id[
genomic_pos_source_hg19['id']]
genomic_pos_ref_hg19 = make_ref_source(
genomic_pos_source_hg19,
PROPS[genomic_pos_id_prop_hg19],
self.external_ids[genomic_pos_id_prop_hg19],
login=self.login)
assembly_hg19 = wdi_core.WDItemID("Q21067546",
PROPS['genomic assembly'],
is_qualifier=True)
chrom_wdid_hg19 = self.chr_num_wdid[genomic_pos_value_hg19['chr']]
qualifiers_hg19 = [
wdi_core.WDItemID(chrom_wdid_hg19,
PROPS['chromosome'],
is_qualifier=True), assembly_hg19
]
strand_orientation_hg19 = 'Q22809680' if genomic_pos_value_hg19[
'strand'] == 1 else 'Q22809711'
else:
do_hg19 = False
strand_orientation_hg19 = None
assembly_hg19 = None
genomic_pos_ref_hg19 = None
genomic_pos_value_hg19 = None
qualifiers_hg19 = None
chrom_wdid_hg19 = None
s = []
# strand orientation
# if the same for both assemblies, only put one statement
if do_hg19 and strand_orientation == strand_orientation_hg19:
s.append(
wdi_core.WDItemID(strand_orientation,
PROPS['strand orientation'],
references=[genomic_pos_ref],
qualifiers=[assembly, assembly_hg19]))
else:
s.append(
wdi_core.WDItemID(strand_orientation,
PROPS['strand orientation'],
references=[genomic_pos_ref],
qualifiers=[assembly]))
if do_hg19:
s.append(
wdi_core.WDItemID(strand_orientation_hg19,
PROPS['strand orientation'],
references=[genomic_pos_ref_hg19],
qualifiers=[assembly_hg19]))
# genomic start and end for both assemblies
s.append(
wdi_core.WDString(str(int(genomic_pos_value['start'])),
PROPS['genomic start'],
references=[genomic_pos_ref],
qualifiers=qualifiers))
s.append(
wdi_core.WDString(str(int(genomic_pos_value['end'])),
PROPS['genomic end'],
references=[genomic_pos_ref],
qualifiers=qualifiers))
if do_hg19:
s.append(
wdi_core.WDString(str(int(genomic_pos_value_hg19['start'])),
PROPS['genomic start'],
references=[genomic_pos_ref_hg19],
qualifiers=qualifiers_hg19))
s.append(
wdi_core.WDString(str(int(genomic_pos_value_hg19['end'])),
PROPS['genomic end'],
references=[genomic_pos_ref_hg19],
qualifiers=qualifiers_hg19))
# chromosome
# if the same for both assemblies, only put one statement
if do_hg19 and chrom_wdid == chrom_wdid_hg19:
s.append(
wdi_core.WDItemID(chrom_wdid,
PROPS['chromosome'],
references=[genomic_pos_ref],
qualifiers=[assembly, assembly_hg19]))
else:
s.append(
wdi_core.WDItemID(chrom_wdid,
PROPS['chromosome'],
references=[genomic_pos_ref],
qualifiers=[assembly]))
if do_hg19:
s.append(
wdi_core.WDItemID(chrom_wdid_hg19,
PROPS['chromosome'],
references=[genomic_pos_ref_hg19],
qualifiers=[assembly_hg19]))
return s
def create_statements(self):
"""
create statements common to all genes
"""
s = []
############
# ID statements (required)
############
entrez_ref = make_ref_source(self.record['entrezgene']['@source'],
PROPS['Entrez Gene ID'],
self.external_ids['Entrez Gene ID'],
login=self.login)
s.append(
wdi_core.WDString(self.external_ids['Entrez Gene ID'],
PROPS['Entrez Gene ID'],
references=[entrez_ref]))
# optional ID statements
ensembl_ref = None
if 'Ensembl Gene ID' in self.external_ids:
ensembl_ref = make_ref_source(self.record['ensembl']['@source'],
PROPS['Ensembl Gene ID'],
self.external_ids['Ensembl Gene ID'],
login=self.login)
s.append(
wdi_core.WDString(self.external_ids['Ensembl Gene ID'],
PROPS['Ensembl Gene ID'],
references=[ensembl_ref]))
# no ensembl transcript ID unless ensembl gene is there also
if 'Ensembl Transcript ID' in self.external_ids:
for id in self.external_ids['Ensembl Transcript ID']:
s.append(
wdi_core.WDString(id,
PROPS['Ensembl Transcript ID'],
references=[ensembl_ref]))
key = 'RefSeq RNA ID'
if key in self.external_ids:
for id in self.external_ids[key]:
s.append(
wdi_core.WDString(id, PROPS[key], references=[entrez_ref]))
for key in [
'NCBI Locus tag', 'Saccharomyces Genome Database ID',
'Mouse Genome Informatics ID', 'MGI Gene Symbol',
'HomoloGene ID', 'Rat Genome Database ID', 'FlyBase Gene ID',
'Wormbase Gene ID', 'ZFIN Gene ID'
]:
if key in self.external_ids:
s.append(
wdi_core.WDString(self.external_ids[key],
PROPS[key],
references=[entrez_ref]))
############
# Gene statements
############
# if there is an ensembl ID, this comes from ensembl, otherwise, entrez
gene_ref = ensembl_ref if ensembl_ref is not None else entrez_ref
# instance of gene
s.append(
wdi_core.WDItemID('Q7187',
PROPS['instance of'],
references=[gene_ref])) # instance of 'gene'
# found in taxon
s.append(
wdi_core.WDItemID(self.organism_info['wdid'],
PROPS['found in taxon'],
references=[gene_ref]))
return s
