usage = """
%prog $Filename $Taxonomy
"""
# argv
fi = sys.argv[1] # Filename, fi = 'entrezgene.txt'
ti = sys.argv[2] # Taxonomy, ti = '10116'
# load
Entrez.email = "*****@*****.**"
handle = Entrez.efetch(db="Taxonomy", id=ti, retmode="xml")
records = Entrez.read(handle)
si = records[0]["ScientificName"] # Specics_Id, si = 'Rattus norvegicus'
mg = mygene.MyGeneInfo()
kg = KEGG()
kt = str(kg.lookfor_organism(si)).replace("u'",
"").split(" ")[1] # KEGG_Taxonomy
kge = kg.list(kt)
# init
lq = [] # List_Query
if fi == "-":
for ln in sys.stdin:
lq.append(ln.strip('\n'))
else:
f = open(fi, 'r')
for ln in f:
lq.append(ln.strip('\n'))
lf = [
'entrezgene', 'ensembl.gene', 'symbol', 'name', 'alias', 'summary',
'refseq', 'unigene', 'ensembl.transcript', 'ensembl.protein', 'uniprot',
'interpro', 'go'
] # List_Field
class KEGGPathways:
"""
KEGG PATHWAY Database API
"""
def __init__(self, organism="H**o sapiens"):
self.database = KEGG()
self.organism = self.get_organism_code(organism.lower())
def search_by_gene(self, gene_name: str):
"""
Args:
gene_name: gene name (ex. 'BRCA2')
Returns:
Dictionary with ids of all pathways containing given gene as keys and their full names as values.
"""
try:
pathways = self.database.get_pathway_by_gene(
gene_name, self.organism)
return pathways if pathways else {}
except AttributeError:
return {}
def get_pathway(self, pathway_id: str, self_loops: bool = False):
"""
Args:
pathway_id: KEGG pathway id (ex. 'hsa04110')
self_loops: information about whether or not include self loops in returned graph
Returns:
`networkx.DiGraph` object: Directed graph depicting pathway, with a comma-separated string
containing gene names as graph nodes and directed edges representing interactions between genes.
Each edge has weight 'type', which is a list of interaction types between two nodes.
"""
G = nx.DiGraph()
try:
pathway = self.database.parse_kgml_pathway(pathway_id)
except TypeError:
# incorrect pathway_id
pathway = None
if pathway:
names = {}
for entry in pathway['entries']:
# only intra-pathway interactions taken into account
if entry['gene_names']:
names[entry['id']] = {
'name': entry['gene_names'],
'type': entry['type']
}
for rel in pathway['relations']:
if rel['entry1'] in names.keys(
) and rel['entry2'] in names.keys():
e1 = names[rel['entry1']]['name']
e2 = names[rel['entry2']]['name']
G.add_node(e1, type=names[rel['entry1']]['type'])
G.add_node(e2, type=names[rel['entry2']]['type'])
if G.has_edge(e1, e2):
G[e1][e2]['type'] = G[e1][e2]['type'] + [rel['name']]
else:
# assumption of interaction direction entry1 -> entry2 #TODO: validate
if e1 != e2 or (e1 == e2 and self_loops):
G.add_edge(e1, e2, type=[rel['name']])
not_gene_nodes = []
for node in G.nodes():
# only interactions between genes
if G.node[node]['type'] != 'gene':
for in_edge in G.in_edges(node):
for out_edge in G.out_edges(node):
if in_edge[0] != out_edge[1] or (
in_edge[0] == out_edge[1] and self_loops):
G.add_edge(in_edge[0],
out_edge[1],
type=['indirect'])
not_gene_nodes.append(node)
G.remove_nodes_from(not_gene_nodes)
return G
def fetch_organism_codes(self):
"""
Returns:
Dictionary with organisms as keys, and KEGG organism codes as values
{ 'h**o sapiens' : 'hsa',
'human' : 'hsa',
...
}
"""
codes = {}
for line in self.database.list('organism').split('\n'):
if line:
code = line.split('\t')[1]
org = line.split('\t')[2]
if '(' in org:
org = [x.strip().lower() for x in org[:-1].split('(')]
for o in org:
codes[o] = code
else:
codes[org] = code
return codes
def get_organism_code(self, org: str):
"""
Args:
org: organism name (ex. 'H**o sapiens', 'human') - lowercase and uppercase optional
Returns:
str: KEGG organism code
"""
codes = self.fetch_organism_codes()
try:
return codes[org]
except KeyError:
print('Invalid organism name.')
raise
def get_gene_code(self, gen: str):
"""
Args:
gen: gene name (ex. 'FGR', 'NIPAL1')
Returns:
KEGG gene code
"""
code_gen = self.database.find(self.organism, gen)
if code_gen == str('\n'):
code_gen = str()
print('Invalid gene name: ' + str(gen))
return code_gen
