feat: match genes ids

docker-compose.yml

@@ -4,7 +4,7 @@ db:
     - 7474:7474
     - 7687:7687
   volumes:
-    - 'cleandb:/data'
+    - '/Users/svegal/neo4j_backup:/data'
   environment:
     - NEO4J_AUTH=neo4j/1
 web:

id_mapper/graph.py

@@ -20,23 +20,22 @@ def __str__(self):
         )
 
 
-def insert_pairs(graph, label, pair1, pair2):
+def insert_pairs(graph, label, pair1, pair2, organism=None):
     """Merge nodes to database and create mutual IS relationships between
 
     :param graph: Graph
     :param label: "Metabolite" or "Reaction"
     :param pair1: node 1
     :param pair2: node 2
+    :param organism: str
     :return:
     """
-    nodes = [
-        Node(
-            label,
-            id=pair.metabolite,
-            db_name=pair.database
-        )
-        for pair in (pair1, pair2)
-        ]
+    nodes = []
+    for pair in (pair1, pair2):
+        kwargs = dict(id=pair.metabolite, db_name=pair.database)
+        if organism:
+            kwargs['organism'] = organism
+        nodes.append(Node(label, **kwargs))
     for n in nodes:
         graph.merge(n)
     graph.merge(Is(nodes[0], nodes[1]))
@@ -55,7 +54,7 @@ def find_match(graph, object_id, db_from, db_to):
     selector = NodeSelector(graph)
     result = []
     found = False
-    for labels in ('Metabolite', 'Reaction'):
+    for labels in ('Metabolite', 'Reaction', 'Gene'):
         selected = list(selector.select(labels, id=object_id, db_name=db_from))
         assert len(selected) <= 1
         if selected:

id_mapper/metanetx.py

@@ -11,7 +11,7 @@ def make_pairs(line):
     ready to be uploaded to the graph database
     """
     xref, metanetx_id = line.split()[:2]
-    xref_db, xref_id = xref.split(':')
+    xref_db, xref_id = xref.split(':', maxsplit=1)
     return Pair(xref_id, xref_db), Pair(metanetx_id, 'mnx')
 
 

load_chem.py

@@ -0,0 +1,25 @@
+import os
+from id_mapper.metanetx import make_pairs
+from id_mapper.graph import insert_pairs
+from py2neo import Graph
+
+from multiprocessing import Pool
+
+N_PROCESSES = 20
+N_LINES = 100
+
+with open('chem_xref_mini_1.tsv') as f:
+    lines = list(f.readlines())
+
+
+def process_piece(chunk):
+    for line in chunk:
+        x, y = make_pairs(line)
+        if x.metabolite != y.metabolite:
+            insert_pairs(graph, 'Metabolite', x, y)
+
+graph = Graph(host=os.environ['DB_PORT_7687_TCP_ADDR'], password=os.environ['NEO4J_PASSWORD'])
+
+with Pool(processes=N_PROCESSES) as pool:
+    pool.map(process_piece, [lines[i:i+N_LINES] for i in range(0, len(lines), N_LINES)])
+

load_gene.py

@@ -0,0 +1,49 @@
+import os
+from id_mapper.metanetx import make_pairs, Pair
+from id_mapper.graph import insert_pairs
+from py2neo import Graph
+import re
+
+from multiprocessing import Pool
+
+N_PROCESSES = 20
+N_LINES = 100
+
+with open('ecodata.txt') as f:
+    lines = list(f.readlines())
+
+DATABASES = ['ecogene', 'eck', 'name', 'syn', 'genbank', 'sp', 'blattner', 'asap', 'genobase', 'cg']
+
+
+def process_piece(chunk):
+    for line in chunk:
+        info = dict(zip(DATABASES, line.split('\t')))
+        to_delete = []
+        for key, value in info.items():
+            if value in ('None', 'Null', 'Null\n', 'null', 'null\n'):
+                to_delete.append(key)
+            else:
+                info[key] = info[key].strip("'; ").strip()
+                info[key] = re.sub('\(\w\.\w\.\)', '', info[key])
+        for key in to_delete:
+            info.pop(key)
+        info['name'] = [info['name']]
+        if 'syn' in info:
+            info['name'].extend(info['syn'].split(', '))
+            info.pop('syn')
+            info['name'] = [i.strip() for i in info['name']]
+        pair_1 = Pair(info['blattner'], 'blattner')
+        for key, value in info.items():
+            if key != 'blattner':
+                if key != 'name':
+                    insert_pairs(graph, 'Gene', pair_1, Pair(value, key), organism='ecoli')
+                else:
+                    for n in value:
+                        insert_pairs(graph, 'Gene', pair_1, Pair(n, key), organism='ecoli')
+
+
+graph = Graph(host=os.environ['DB_PORT_7687_TCP_ADDR'], password=os.environ['NEO4J_PASSWORD'])
+
+with Pool(processes=N_PROCESSES) as pool:
+    pool.map(process_piece, [lines[i:i+N_LINES] for i in range(0, len(lines), N_LINES)])
+