gene_hgnc_id = 'HGNC:' + row[3]
gene_entrez_id = int(row[4])
gene_entrez_id = 'Entrez:' + str(gene_entrez_id)
pmid = int(row[8])
pmid = str(pmid)
with io.open(mirna_to_URS_mapping_file, 'r', encoding='utf-8', newline='') as mapping_file:
mapping_reader = csv.reader(mapping_file, delimiter='\t')
next(mapping_reader, None)
for mapping_row in mapping_reader:
if mirna_name == mapping_row[2]:
mirna_rnacentral_id = mapping_row[0]
mirna = MiRNA([mirna_rnacentral_id], [mirna_name])
network.add_node(mirna)
gene = Gene([gene_hgnc_id, gene_entrez_id], [])
network.add_node(gene)
if (mirna_rnacentral_id + '$' + gene_hgnc_id) in edge_source_target_lookup:
edges = network.get_edges_from_to(mirna, gene, 'REGULATES')
for edge in edges:
pmid = edge.attributes['pmid'] + ', ' + str(pmid)
network.delete_edge(edge)
e = Edge(mirna, gene, 'REGULATES', {'source': 'miRTarBase', 'pmid': pmid})
network.add_edge(e)
edge_source_target_lookup.append(mirna_rnacentral_id + '$' + gene_hgnc_id)
else:
e = Edge(mirna, gene, 'REGULATES', {'source': 'miRTarBase', 'pmid': pmid})
network.add_edge(e)
edge_source_target_lookup.append(mirna_rnacentral_id + '$' + gene_hgnc_id)
break
network.save('data/miRTarBase/graph.json')
gene_hgnc_id = 'HGNC:' + gene_mapping_row[1]
break
if gene_hgnc_id != 'None' and 'gene' in row[21]:
gene_uniprotkb_id = re.split('[:(]', row[5])
gene_uniprotkb_id = 'UniProtKB:' + gene_uniprotkb_id[1]
gene_ensembl_id = 'Ensembl:' + gene_ensembl_id
gene = Gene([gene_hgnc_id, gene_uniprotkb_id, gene_ensembl_id],
[])
network.add_node(gene)
pmid = row[8].split(':')
pmid = pmid[1]
source_database = row[12]
source_database = source_database.replace('\"', '')
if (mirna_rnacentral_id + '$' +
gene_hgnc_id) in edge_source_target_lookup:
reg_edges = network.get_edges_from_to(
mirna, gene, 'REGULATES')
for reg_edge in reg_edges:
if reg_edge.attributes['source'] == (
'EBI-GOA-miRNA, ' + source_database):
pmid = reg_edge.attributes['pmid'] + ', ' + pmid
network.delete_edge(reg_edge)
e = Edge(
mirna, gene, 'REGULATES', {
'source':
'EBI-GOA-miRNA, ' + source_database,
'pmid': pmid
})
network.add_edge(e)
edge_source_target_lookup.append(
mirna_rnacentral_id + '$' + gene_hgnc_id)
else:
drug, 'CONTRAINDICATES')
}
if not indications.isdisjoint(contraindications):
drug_check_failed_count += 1
for intersection in indications.intersection(
contraindications):
disease = network.get_node_by_id(intersection, 'Disease')
drug_text = '%s<br/>%s' % (node_ids_to_links(
drug.ids), '<br/>'.join(drug.names))
indications_text = '<br/>'.join([
'%s: %s -> %s' %
(x.attributes['source'],
node_ids_to_links([x.source_node_id]),
node_ids_to_links([x.target_node_id]))
for x in network.get_edges_from_to(
drug, disease, 'INDICATES')
])
contraindications_text = '<br/>'.join([
'%s: %s -> %s' %
(x.attributes['source'],
node_ids_to_links([x.source_node_id]),
node_ids_to_links([x.target_node_id]))
for x in network.get_edges_from_to(
drug, disease, 'CONTRAINDICATES')
])
f.write(
'<tr><td>%s</td><td style="white-space: nowrap;">%s</td><td style="white-space: nowrap;">%s</td></tr>\n'
%
(drug_text, indications_text, contraindications_text))
f.write('</tbody>\n</table>\n')
