def load_data(data_folder):
input_file = os.path.join(data_folder, "all_cell_markers.txt")
assert os.path.exists(input_file), "Can't find input file '{}'".format(input_file)
with open_anyfile(input_file) as in_f:
header = next(in_f).strip().split('\t')
reader = DictReader(in_f, fieldnames=header, delimiter='\t')
for row in reader:
for field in ['cellMarker', 'geneID', 'geneSymbol', 'proteinID', 'proteinName']:
row[field] = parse_field(row[field])
if not all([
len(row['cellMarker']) == len(row['geneID']),
len(row['cellMarker']) == len(row['geneSymbol']),
len(row['cellMarker']) == len(row['proteinID']),
len(row['cellMarker']) == len(row['proteinName'])]):
# handle weird cases...
pass
else:
# they all match
for index in range(len(row['cellMarker'])):
r = copy.copy(row)
for field in ['cellMarker', 'geneID', 'geneSymbol', 'proteinID', 'proteinName']:
r[field] = r[field][index]
_id = generate_id(r)
yield {"_id": _id,
"CellMarker": r}
def load_data(data_folder, assembly="hg19"):
"""Load data from EMV csv file into list of JSON docs
"""
input_file = os.path.join(data_folder, "EmVClass.2018-Q2.csv")
assert os.path.exists(
input_file), "Can't find input file '%s'" % input_file
with open_anyfile(input_file) as in_f:
lines = set(list(in_f))
lines = [_doc.strip().split(',') for _doc in lines]
print(list(lines)[0])
results = defaultdict(list)
# mapping non genomic hgvs ids to genomic hgvs ids used in MyVariant
hgvs_ids = [_item[4] for _item in lines]
#print(hgvs_ids)
hgvs_mapping_dict = batch_query_myvariant_id_from_clingen(
hgvs_ids, assembly)
# loop through csv doc to convert into json docs
for row in lines:
# structure the content of emv docs
variant = _map_line_to_json(row)
# fetch corresponding genomic hgvs ids
mapped_ids = hgvs_mapping_dict[row[4]]
# could be one non-genomic hgvs id mapping to mulitple genomic ones
if mapped_ids:
for _id in mapped_ids:
results[_id].append(variant)
for k, v in results.items():
if len(v) == 1:
doc = {'_id': k, 'emv': v[0]}
else:
doc = {'_id': k, 'emv': [_doc for _doc in v]}
print('case of multi hits', doc)
yield doc
def load_data(data_folder):
input_file = os.path.join(data_folder, "cgi_biomarkers_per_variant.tsv")
assert os.path.exists(
input_file), "Can't find input file '%s'" % input_file
with open_anyfile(input_file) as in_f:
# Remove duplicated lines if any
header = next(in_f).strip().split('\t')
lines = set(list(in_f))
reader = DictReader(lines, fieldnames=header, delimiter='\t')
results = defaultdict(list)
for row in reader:
variant = {}
# Skip
if 'gDNA' not in row or row['gDNA'] == "":
continue
# Skip variants that are not mutations
if 'Alteration type' not in row or row['Alteration type'] != 'MUT':
continue
# Use gDNA as variant identifier
variant['_id'] = row['gDNA']
variant['cgi'] = {}
for k in [
'region', 'cDNA', 'Evidence level', 'transcript', 'Gene',
('individual_mutation', 'protein_change'),
'Primary Tumor type', ('Drug full name', 'drug'), 'Source',
'Association'
]:
if isinstance(k, tuple):
new_k = k[1]
old_k = k[0]
else:
new_k = k.lower().replace(' ', '_')
old_k = k
variant['cgi'][new_k] = unicodedata.normalize(
"NFKD", row.get(old_k, None))
variant = dict_sweep(variant,
vals=['', 'null', 'N/A', None, [], {}])
results[variant['_id']].append(variant)
# Merge duplications
for v in results.values():
if len(v) == 1:
yield v[0]
else:
yield {'_id': v[0]['_id'], 'cgi': [i['cgi'] for i in v]}
def load_data(input_file):
with open_anyfile(input_file) as in_f:
for line in in_f:
_id, caid = line.strip().split()
yield {
'_id': _id,
'clingen': {
"caid": caid
},
}
def load_data(input_file):
with open_anyfile(input_file) as in_f:
result = defaultdict(list)
for line in in_f:
pharos_id, _id = line.strip().split(',')
if _id != 'entrez_gene_id' and _id != '0':
result[str(_id)].append(int(pharos_id))
for k, v in result.items():
json_doc = {'_id': str(k), 'pharos': {"target_id": v}}
yield unlist(json_doc)
def load_data(input_file):
with open_anyfile(input_file) as in_f:
for line in in_f:
pharos_id, _id = line.strip().split(',')
if _id != 'entrez_gene_id':
yield {
'_id': int(_id),
'pharos': {
"target_id": int(pharos_id)
},
}
def load_data(data_folder):
input_file = os.path.join(data_folder, "phewas-catalog.csv")
assert os.path.exists(input_file), "Can't find input file '%s'" % input_file
with open_anyfile(input_file) as in_f:
# Remove duplicated lines if any
header = next(in_f).strip().split(',')
header = [_item[1:-1] for _item in header]
lines = set(list(in_f))
reader = DictReader(lines, fieldnames=header, delimiter=',')
results = defaultdict(list)
for row in reader:
variant = {"associations": {"phenotype": {}}, "variant": {}}
assert re.match("^rs\d+$", row["snp"]) != None
variant["variant"]["rsid"] = row["snp"]
variant["associations"]["phenotype"]["name"] = row["phewas phenotype"]
variant["associations"]["cases"] = row["cases"]
variant["associations"]["pval"] = float(row["p-value"])
variant["associations"]["odds-ratio"] = row["odds-ratio"]
variant["associations"]["phenotype"]["phewas_code"] = row["phewas code"]
variant["variant"]["gene"] = row["gene_name"]
variant["variant"]["gwas_associations"] = row["gwas-associations"].split(',')
pos_info = row["chromosome"].split(' ')
if len(pos_info) == 2:
variant["variant"]["chrom"], variant["variant"]["pos"] = pos_info
else:
variant["variant"]["chrom"] = pos_info[0]
results[variant["variant"]["rsid"]].append(variant)
# Merge duplications
rsid_list = [_item for _item in results.keys()]
hgvs_rsid_dict = batch_query_hgvs_from_rsid(rsid_list)
for k, v in results.items():
if k in hgvs_rsid_dict and hgvs_rsid_dict[k]:
if len(v) == 1:
doc = {'_id': hgvs_rsid_dict[k],
'phewas': v[0]["variant"]}
doc["phewas"]["associations"] = v[0]["associations"]
yield dict_sweep(unlist(value_convert_to_number(doc, skipped_keys=['chrom'])), vals=[[], {}, None, '', 'NULL'])
else:
doc = {'_id': hgvs_rsid_dict[k],
'phewas': v[0]["variant"]}
doc["phewas"]["associations"] = []
for _item in v:
doc["phewas"]["associations"].append(_item["associations"])
yield dict_sweep(unlist(value_convert_to_number(doc, skipped_keys=['chrom'])), vals=[[], {}, None, '', 'NULL'])
def load_data(data_folder: str):
"""
Load data from a specified file path. Parse each line into a dictionary according to the schema
given by `data_schema`. Then process each dict by normalizing data format, remove null fields (optional).
Append each dict into final result using its id.
:param data_folder: the path(folder) where the data file is stored
:return: a generator that yields data.
"""
input_file = os.path.join(data_folder, file_name)
# raise an error if file not found
assert os.path.exists(input_file), FILE_NOT_FOUND_ERROR.format(input_file)
with open_anyfile(input_file) as file:
# Remove duplicated lines if any
lines = set(list(file))
# read and parse each line into a dict
reader = DictReader(lines, fieldnames=data_schema, delimiter=delimiter)
# access non existing keys will return an empty list by default
results = defaultdict(list)
for row in reader: # start processing each lines of data (stored in dicts)
# construct id (e.g. chr1:g.678900_679000)
_id = '{chrom}:g.{start}_{end}'.format(chrom=row['chrom'],
start=row['start'],
end=row['end'])
# optional step: normalize data
variant = {
k: unicodedata.normalize('NFKD', v)
for k, v in row.items()
}
# optional step: delete invalid fields within each dict
variant = dict_sweep(variant,
vals=['', 'null', 'N/A', None, [], {}])
# append dict to the result list using the _id
results[_id].append(variant)
for k, v in results.items():
yield {'_id': k, source_name: v}
def load_data(data_folder):
input_file = os.path.join(data_folder, "alternative")
# input_file = os.path.join(data_folder, "gwas_catalog_v1.0.2-associations_e96_r2019-04-21.tsv")
assert os.path.exists(
input_file), "Can't find input file '%s'" % input_file
with open_anyfile(input_file) as in_f:
# Remove duplicated lines if any
header = next(in_f).strip().split('\t')
lines = set(list(in_f))
reader = DictReader(lines, fieldnames=header, delimiter='\t')
results = defaultdict(list)
rsid_list = []
for row in reader:
rsids, _ = parse_separator_and_snps(row)
if rsids:
rsid_list += rsids
hgvs_rsid_dict = batch_query_hgvs_from_rsid(rsid_list)
reader = DictReader(lines, fieldnames=header, delimiter='\t')
for row in reader:
variant = {}
HGVS = False
snps, seperator = parse_separator_and_snps(row)
if not snps:
continue
region = reorganize_field(row["REGION"], seperator, len(snps))
chrom = reorganize_field(row["CHR_ID"], seperator, len(snps))
genes = reorganize_field(row["REPORTED GENE(S)"], seperator,
len(snps))
position = reorganize_field(row["CHR_POS"], seperator, len(snps))
context = reorganize_field(row["CONTEXT"], seperator, len(snps))
for i, _snp in enumerate(snps):
variant = {}
if _snp in hgvs_rsid_dict:
variant["_id"] = hgvs_rsid_dict[_snp]
else:
continue
variant['gwascatalog'] = {
"associations": {
'efo': {},
'study': {}
}
}
if not HGVS:
variant["gwascatalog"]["rsid"] = _snp
variant['gwascatalog']['associations']['snps'] = snps
variant['gwascatalog']['associations']['pubmed'] = int(
row['PUBMEDID'])
variant['gwascatalog']['associations']['date_added'] = row[
'DATE ADDED TO CATALOG']
variant['gwascatalog']['associations']['study']['name'] = row[
'STUDY']
variant['gwascatalog']['associations']['trait'] = row[
'DISEASE/TRAIT']
variant['gwascatalog'][
'region'] = region[i] if region else None
if not chrom:
chrom = [''] * 10
elif str(chrom[i]).lower() not in CHROM_LIST:
chrom[i] = ''
variant['gwascatalog']['chrom'] = chrom[i] if chrom else None
variant['gwascatalog'][
'pos'] = position[i] if position else None
variant['gwascatalog']['gene'] = genes[i].split(',') if (
genes and genes[i]) else None
variant['gwascatalog'][
'context'] = context[i] if context else None
variant['gwascatalog']['associations']['raf'] = str2float(
row['RISK ALLELE FREQUENCY'])
variant['gwascatalog']['associations']['pval'] = str2float(
row['P-VALUE'])
# variant['gwascatalog']['p_val_mlog'] = str2float(row['PVALUE_MLOG'])
variant['gwascatalog']['associations']['study'][
'platform'] = row['PLATFORM [SNPS PASSING QC]']
variant['gwascatalog']['associations']['study'][
'accession'] = row['STUDY ACCESSION']
variant['gwascatalog']['associations']['efo']['name'] = row[
'MAPPED_TRAIT'].split(',')
variant['gwascatalog']['associations']['efo']['id'] = [
_item.split('/')[-1].replace('_', ':')
for _item in row['MAPPED_TRAIT_URI'].split(',')
]
variant = dict_sweep(unlist(
value_convert_to_number(variant, skipped_keys=['chrom'])),
vals=[[], {}, None, '', 'NR'])
results[variant["_id"]].append(variant)
for v in results.values():
if len(v) == 1:
yield v[0]
else:
doc = {'_id': v[0]['_id'], 'gwascatalog': {'associations': []}}
for _item in ['gene', 'region', 'pos', 'context', 'rsid']:
if _item in v[0]['gwascatalog']:
doc['gwascatalog'][_item] = v[0]['gwascatalog'][_item]
doc['gwascatalog']['associations'] = [
i['gwascatalog']['associations'] for i in v
]
yield doc
def parse_data(data_access):
"""
return: a list containing a nested dinctionary with ENTREZ ID as gene ID
"""
current_time = date.today().strftime("-%Y-%m-%d")
file_name = "ClinGen-Gene-Disease-Summary{}.csv".format(str(current_time))
data_dir = os.path.join(data_access, file_name)
# check if the file exist
assert os.path.exists(
data_dir), "input file '%s' does not exist" % data_dir
# read file
with open_anyfile(data_dir) as input_file:
for _ in range(4):
next(input_file)
header = next(input_file).strip().split(",")
next(input_file)
reader = csv.DictReader(set(list(input_file)),
fieldnames=header,
delimiter=",")
output = defaultdict(list)
# initialize a list to store HGNC ID
#hgnc_list = []
for row in reader:
# skip samples with empty HGNC
if not 'GENE ID (HGNC)' in row or not row['GENE ID (HGNC)']:
continue
# store HGNC gen ID for conversion
hgnc_id = row['GENE ID (HGNC)'].split(':')[1]
#hgnc_list.append(hgnc_id)
# store every gene's information into a nested dictionary
gene = {}
gene['_id'] = hgnc_id
gene['clingen'] = {}
gene['clingen']['clinical_validity'] = {}
key_list = [
'DISEASE LABEL', 'DISEASE ID (MONDO)', 'SOP', 'CLASSIFICATION',
'ONLINE REPORT'
]
# for each key, store the value into the gene dictionary
for key in key_list:
# disease value: "MONDO_ID" -> "MONDO:ID"
if key == 'DISEASE ID (MONDO)':
old_key = key
complete_key = 'mondo'
gene['clingen']['clinical_validity'][
complete_key] = row.get(old_key,
None).replace("_", ":")
elif key == 'CLASSIFICATION':
old_key = key
complete_key = key.lower().replace(
' ', '_') # key to lower case
gene['clingen'][
'clinical_validity'][complete_key] = row.get(
old_key, None).lower() # value to lower case
else:
old_key = key
complete_key = key.lower().replace(
' ', '_') # key to lower case
gene['clingen']['clinical_validity'][
complete_key] = row.get(old_key, None)
gene = dict_sweep(gene, vals=['', 'null', 'N/A', None, [], {}])
output[gene['_id']].append(gene)
#entrez_hgnc_dict = hgnc2entrenz(hgnc_list)
temp_output = []
# merge duplicates, this amy happen when a gene causes multiple diseases amd has multiple labels
for value in output.values():
# genes without duplicate
if len(value) == 1:
temp_output.append(value[0])
# genes in duplicate
else:
temp_output.append({
'_id': value[0]['_id'],
'clingen': {
'clinical_validity':
[v['clingen']['clinical_validity'] for v in value]
}
})
return hgnc2entrez(temp_output)
