continue
if source_uniprot not in nodes:
source = {
"name": "uniprot:" + source_uniprot,
"alt_accession": "",
"tax_id": "taxid:99284",
"pathways": "",
"aliases": "",
"topology": "",
}
nodes[source_uniprot] = source
nodes[source_uniprot]["id"] = db_api.insert_node(source)
if target_uniprot not in nodes:
target = {
"name": "uniprot:" + target_uniprot,
"alt_accession": "",
"tax_id": "taxid:99284",
"pathways": "",
"aliases": "",
"topology": "",
}
nodes[target_uniprot] = target
nodes[target_uniprot]["id"] = db_api.insert_node(target)
# skipping header
mapFile.readline()
for line in mapFile:
uniprot, salmonella = line.strip().split("\t")
salmonella_nodes[salmonella] = salmonella_node ={
'name': "uniprot:" + uniprot,
'alt_accession': "gene symbol:" + salmonella,
'tax_id': "taxid:99284",
'pathways': "",
'aliases': "",
'topology': ""
}
salmonella_nodes[salmonella]["id"] = db_api.insert_node(salmonella_node)
with open(args.source_file) as source_file:
# skipping the header
source_file.readline()
for line in source_file:
salm_node_acc, human_node_acc = line.strip().split(';')
dictionary_cursor.execute("""
SELECT DISTINCT uniprot.accession
FROM uniprot
JOIN foreign_ids on uniprot.id == foreign_ids.uniprot_id
WHERE foreign_ids.accession = ? AND uniprot.is_swissprot = 1
""", (human_node_acc,))
if source_uniprot not in nodes:
source = {
'name' : "uniprot:"+source_uniprot,
'alt_accession' : "",
'tax_id' : "taxid:99284",
'pathways' : "",
'aliases' : "",
'topology' : ""
}
nodes[source_uniprot] = source
nodes[source_uniprot]["id"] = db_api.insert_node(source)
if target_uniprot not in nodes:
target = {
'name' : "uniprot:"+target_uniprot,
'alt_accession' : "",
'tax_id' : "taxid:99284",
'pathways' : "",
'aliases' : "",
'topology' : ""
}
nodes[target_uniprot] = target
nodes[target_uniprot]["id"] = db_api.insert_node(target)
salmonella_uniprot, salmonella_gene_symbol, human_uniprot, human_gene_symbol = linearr
if salmonella_uniprot not in nodes:
salmonella_node = {
'name': "uniprot:" + salmonella_uniprot,
'alt_accession': "gene symbol:" + salmonella_gene_symbol,
'tax_id': "taxid:99284",
'pathways': "",
'aliases': "",
'topology': ""
}
nodes[salmonella_uniprot] = salmonella_node
nodes[salmonella_uniprot]["id"] = db_api.insert_node(
salmonella_node)
if human_uniprot not in nodes:
human_node = {
'name': "uniprot:" + human_uniprot,
'alt_accession': "gene symbol:" + human_gene_symbol,
'tax_id': "taxid:9606",
'pathways': "",
'aliases': "",
'topology': ""
}
nodes[human_uniprot] = human_node
nodes[human_uniprot]["id"] = db_api.insert_node(human_node)
# skipping header
mapFile.readline()
for line in mapFile:
uniprot, salmonella = line.strip().split("\t")
salmonella_nodes[salmonella] = salmonella_node = {
'name': "uniprot:" + uniprot,
'alt_accession': "gene symbol:" + salmonella,
'tax_id': "taxid:99284",
'pathways': "",
'aliases': "",
'topology': ""
}
salmonella_nodes[salmonella]["id"] = db_api.insert_node(
salmonella_node)
with open(args.source_file) as source_file:
# skipping the header
source_file.readline()
for line in source_file:
salm_node_acc, human_node_acc = line.strip().split(';')
dictionary_cursor.execute(
"""
SELECT DISTINCT uniprot.accession
FROM uniprot
JOIN foreign_ids on uniprot.id == foreign_ids.uniprot_id
WHERE foreign_ids.accession = ? AND uniprot.is_swissprot = 1
linearr = line.split("\t")
# deconstructing the array generated from the line
node_id, name, alt_accession, tax_id, pathways, aliases, topology = linearr
node_dict = {
'name' : name,
'alt_accession' : alt_accession,
'tax_id' : tax_id,
'pathways' : pathways,
'aliases' : aliases,
'topology' : topology
}
node_dict['id'] = db_api.insert_node(node_dict)
nodes[name] = node_dict
print("Parsing nodes done.")
# parsing edges
with open(args.edge_source_file) as edge_file:
# informing the user
print "Parsing edges"
sum_edges = sum([1 for line in edge_file])
progress = 1
edge_file.seek(0)
source_name = linearr[1]
if source_name not in nodes:
source = {
'name' : "uniprot:"+source_name,
'alt_accession' : "gene symbol:"+linearr[0],
'tax_id' : "taxid:"+linearr[2],
'pathways' : linearr[7],
'aliases' : "",
'topology' : linearr[4]
}
nodes[source_name] = source
source_id = db_api.insert_node(source)
nodes[source_name]["id"] = source_id
target_name = linearr[9]
if target_name not in nodes:
target = {
'name' : "uniprot:"+target_name,
'alt_accession' : "gene symbol:"+linearr[8],
'tax_id' : "taxid:"+linearr[10],
'pathways' : linearr[15],
'aliases' : "",
'topology' : linearr[12]
salmonella_uniprot, salmonella_gene_symbol, human_uniprot, human_gene_symbol = linearr
if salmonella_uniprot not in nodes:
salmonella_node = {
"name": "uniprot:" + salmonella_uniprot,
"alt_accession": "gene symbol:" + salmonella_gene_symbol,
"tax_id": "taxid:99284",
"pathways": "",
"aliases": "",
"topology": "",
}
nodes[salmonella_uniprot] = salmonella_node
nodes[salmonella_uniprot]["id"] = db_api.insert_node(salmonella_node)
if human_uniprot not in nodes:
human_node = {
"name": "uniprot:" + human_uniprot,
"alt_accession": "gene symbol:" + human_gene_symbol,
"tax_id": "taxid:9606",
"pathways": "",
"aliases": "",
"topology": "",
}
nodes[human_uniprot] = human_node
nodes[human_uniprot]["id"] = db_api.insert_node(human_node)
def main():
for db in args.source_files:
# informing the user
print("Parsing %s" % db)
cursor = sqlite3.connect(db).cursor()
mapped_nodes = {}
nodemap = {}
cursor.execute("SELECT * FROM node")
result = cursor.fetchall()
length = len(result)
current = 1
new_db = PsimiSQL()
cursor.execute("SELECT count(*) FROM node")
num_of_nodes = cursor.fetchone()[0]
# mapping nodes
print("Mapping nodes")
for line in result:
# informing user
if (current % 50 == 0):
print("Mapping nodes %d/%d" % (current, length))
current += 1
row_id, name, alt_accession, tax_id, pathways, aliases, topology = line
old_uniprot = name
new_uniprot = "uniprot:"+get_primary(old_uniprot.split(':')[1])
# storing the new uniprot id for every old id
nodemap[old_uniprot] = new_uniprot
mapped_node = {
'name': new_uniprot,
'alt_accession': alt_accession,
'tax_id': tax_id,
'pathways': pathways,
'aliases': aliases,
'topology': topology
}
mapped_node['id'] = new_db.insert_node(mapped_node)
mapped_nodes[new_uniprot] = mapped_node
if len(nodemap) != num_of_nodes:
print "Gebasz"
# mapping edges
cursor.execute("SELECT * FROM edge")
result = cursor.fetchall()
print("Mapping edges")
length = len(result)
current = 1
shit_counter = 0
for row in result:
if (current % 10 == 0):
print("Parsing edge %d/%d" % (current, length))
current += 1
old_source_uniprot = row[3]
old_target_uniprot = row[4]
edge_dict = {
'interaction_detection_method': row[5],
'first_author': row[6],
'publication_ids': row[7],
'interaction_types': row[8],
'source_db': row[9],
'interaction_identifiers': row[10],
'confidence_scores': row[11],
'layer': "0"
}
if (old_source_uniprot not in mapped_nodes or old_target_uniprot not in mapped_nodes):
shit_counter +=1
else:
new_db.insert_edge(mapped_nodes[old_source_uniprot], mapped_nodes[old_target_uniprot], edge_dict)
# saving the mapped db and informing user
db_name = os.path.split(db)[1]
print("Saving db to %s " % (args.outdir+"/mapped"+db_name))
print("SHITCOUNTER %d" % shit_counter )
new_db.save_db_to_file(args.outdir+"/mapped"+db_name)
