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Update format_ncbi_gene.py
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Fix how Gene dcids are created! Remove extra "dcid:" prefixes and extra quotes around values that are used to serve as dcids to initiate nodes.
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@spiekos
spiekos authored Oct 22, 2024
1 parent 0383db6 commit 2ac3d64
Showing 1 changed file with 18 additions and 18 deletions.
36 changes: 18 additions & 18 deletions scripts/biomedical/NCBI_Gene/scripts/format_ncbi_gene.py
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
Date: 22-Aug-2024
Name: format_ncbi_gene
Edited By: Samantha Piekos
Date: 21-Oct-2024
Date: 22-Oct-2024
Description: cleaning the NCBI Gene data.
@source data: Download Gene data from FTP location. Refer to download.sh for details
"""
Expand Down Expand Up @@ -517,8 +517,8 @@ def process_gene_info(self, file_to_process: str, return_dict) -> None:
end='\r')
row['taxID'] = input_row[0]
row['GeneID'] = input_row[1]
dcid = f"bio/{input_row[1]}" if input_row[
0] != '9606' else f"bio/ncbi_{input_row[1]}"
dcid = f"bio/ncbi_{input_row[1]}" if input_row[
0] != '9606' else f"bio/{input_row[2]}"
dcid = dcid.replace("@", "_Cluster")
row['dcid'] = dcid
gene_id_dcid_mapping[input_row[1]] = dcid
Expand All @@ -527,7 +527,7 @@ def process_gene_info(self, file_to_process: str, return_dict) -> None:
[f'"{x}"' for x in input_row[4].split('|')])
if len(input_row[5]) > 1:
dbs_lst = [x for x in input_row[5].split('|')]
db_obj = {'GeneID': f"dcid:{dcid}"}
db_obj = {'GeneID': f"{dcid}"}
for dbs in dbs_lst:
db = dbs.split(':')
unique_dbXrefs.add(db[0])
Expand Down Expand Up @@ -696,7 +696,7 @@ def process_csv_file(self) -> None:
else:
Gene_PubMedID[input_row[1]] = {
'dcid':
f"dcid:{GENE_ID_DCID_MAPPING[input_row[1]]}",
f"{GENE_ID_DCID_MAPPING[input_row[1]]}",
'PubMedID': [input_row[2]]
}
#Gene_PubMedID[input_row[1]].append()
Expand Down Expand Up @@ -759,7 +759,7 @@ def process_csv_file(self, file_to_process: str) -> None:
print(f"{file_to_process} {input_row[1]}",
end='\r')
row = deepcopy(GENE_NEIGHBORS_DICT)
row['GeneID'] = f"dcid:{GENE_ID_DCID_MAPPING[input_row[1]]}"
row['GeneID'] = f"{GENE_ID_DCID_MAPPING[input_row[1]]}"
row['genomic_accession.version'] = input_row[2]
row['genomic_gi'] = input_row[3]
row['start_position'] = input_row[4]
Expand Down Expand Up @@ -800,15 +800,15 @@ def process_csv_file(self) -> None:
if input_row[1] in Gene_orthologs:
if input_row[4] in GENE_ID_DCID_MAPPING:
Gene_orthologs[input_row[1]]['ortholog'].append(
f'"dcid:{GENE_ID_DCID_MAPPING[input_row[4]]}"'
f'{GENE_ID_DCID_MAPPING[input_row[4]]}'
)
else:
if input_row[4] in GENE_ID_DCID_MAPPING:
Gene_orthologs[input_row[1]] = {
'dcid':
f"dcid:{GENE_ID_DCID_MAPPING[input_row[1]]}",
f'{GENE_ID_DCID_MAPPING[input_row[1]]}',
'ortholog': [
f'"dcid:{GENE_ID_DCID_MAPPING[input_row[4]]}"'
f'{GENE_ID_DCID_MAPPING[input_row[4]]}'
]
}

Expand Down Expand Up @@ -861,7 +861,7 @@ def process_csv_file(self) -> None:
if column_name in Gene_group[input_row[1]]:
try:
Gene_group[input_row[1]][column_name].append(
f'"dcid:{GENE_ID_DCID_MAPPING[input_row[4]]}"'
f'dcid:{GENE_ID_DCID_MAPPING[input_row[4]]}'
)
except:
logging.info(
Expand All @@ -870,7 +870,7 @@ def process_csv_file(self) -> None:
try:
Gene_group[input_row[1]][column_name] = []
Gene_group[input_row[1]][column_name].append(
f'"dcid:{GENE_ID_DCID_MAPPING[input_row[4]]}"'
f'dcid:{GENE_ID_DCID_MAPPING[input_row[4]]}'
)
except:
logging.info(
Expand All @@ -880,9 +880,9 @@ def process_csv_file(self) -> None:
try:
Gene_group[input_row[1]] = {
'GeneID':
f"dcid:{GENE_ID_DCID_MAPPING[input_row[1]]}",
f"{GENE_ID_DCID_MAPPING[input_row[1]]}",
column_name: [
f'"dcid:{GENE_ID_DCID_MAPPING[input_row[4]]}"'
f'dcid:{GENE_ID_DCID_MAPPING[input_row[4]]}'
]
}
except:
Expand Down Expand Up @@ -953,7 +953,7 @@ def process_csv_file(self) -> None:
row['omim_dcid'] = f"bio/omim_{input_row[0]}"
row['type'] = GENE_MIM_TYPE_DIC[input_row[2]]
row['Source'] = ','.join([
f'"{GENE_OMIM_SOURCE_DICT.get(x.strip(), x.strip())}"'
f'{GENE_OMIM_SOURCE_DICT.get(x.strip(), x.strip())}'
for x in input_row[3].strip().split(';')
])
if row['MedGenCUI'].startswith('C'):
Expand All @@ -963,7 +963,7 @@ def process_csv_file(self) -> None:
for c in input_row[5].split(':'):
if c.strip() in GENE_COMMENT_DICT:
cmt.append(
f'"{GENE_COMMENT_DICT[c.strip()]}"')
f'{GENE_COMMENT_DICT[c.strip()]}')
if len(cmt) > 0:
row['Comment'] = ','.join(cmt)
row['dcid'] = f"{dcid}_omim_{input_row[0]}"
Expand Down Expand Up @@ -1011,7 +1011,7 @@ def process_csv_file(self, file_to_process: str) -> None:
end='\r')
row = deepcopy(GENE_GO_DICT)
dcid = GENE_ID_DCID_MAPPING[input_row[1]]
row['GeneID'] = f"dcid:{dcid}"
row['GeneID'] = f"{dcid}"
row['GO_ID'] = input_row[2]
row['dcid'] = f"bio/{input_row[2].replace(':','_')}"
row['Evidence'] = GENE_EVIDENCE_DICT[input_row[3]]
Expand Down Expand Up @@ -1081,7 +1081,7 @@ def process_csv_file(self, file_to_process: str) -> None:
row = deepcopy(GENE_ACCESSION_DICT)

dcid = GENE_ID_DCID_MAPPING[input_row[1]]
row['GeneID'] = f"dcid:{dcid}"
row['GeneID'] = f"{dcid}"
row['dcid_rna_coordinates'] = f"bio/{input_row[3]}_{input_row[9]}_{input_row[10]}"
row['name_rna_coordinates'] = f"{input_row[3]} {input_row[9]} {input_row[10]}"
row['dcid_rna_transcript'] = f"bio/{input_row[3]}"
Expand Down Expand Up @@ -1166,7 +1166,7 @@ def process_csv_file(self) -> None:
print(f"gene2ensembl {input_row[1]}", end='\r')
row = deepcopy(GENE_ENSEMBL_DICT)
dcid = GENE_ID_DCID_MAPPING[input_row[1]]
row['GeneID'] = f"dcid:{dcid}"
row['GeneID'] = f"{dcid}"
row['Ensembl_gene_identifier'] = input_row[2]
if len(input_row[3]) > 0:
row['RNA_nucleotide_accession.version'] = input_row[
Expand Down

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