restructured options of enzyme, GO and SO retriever and edited tags.txt accordingly

providers.yaml

@@ -59,6 +59,9 @@
       xml: ["http://pfam.xfam.org/family/%i?output=xml"]
   # does not work
   # check_existence: "http://pfam.xfam.org/family/%i?content-type=text%2Fxml"
+  retriever:
+      type: 'external'
+      location: 'scripts/retrieve_pfam.py'
 - name: PDB
   prefixes: ["PDB"]
   resources:

scripts/retrieve_enzyme.py

@@ -84,8 +84,7 @@ def main():
 							l[1] = l[1].replace(' ', '')
 							l[1] = l[1].replace(';', '')
 							refs.append(l[0])
-			if len(refs) > 0:
-				output['uniprot'] = refs
+			output['uniprot'] = refs
 		if len(reaction) > 0:
 			if 'reaction_catalysed' in output:
 				output['reaction_catalysed'].append(reaction)
@@ -99,25 +98,33 @@ def main():
 		documents.append(format_output(output, args))
 	print(json.dumps(documents))
 
+def read_basic(d):
+	out = {}
+	definition = {}
+	if 'name' in d:
+		out['name'] = d['name']
+	if 'alternative_names' in d:
+		out['synonyms'] = d.pop('alternative_names')
+	if 'reaction_catalysed' in d:
+		definition['reaction_catalysed'] = d['reaction_catalysed']
+	if 'cofactors' in d:
+		definition['cofactors'] = d['cofactors']
+	if 'comments' in d:
+		definition['comments'] = d['comments']
+	if len(definition) == 1:
+		out['deifinition'] = definition[0]
+	elif len(definition) > 1:
+		out['deifinition'] = definition
+	return (out)
+
 def format_output(d, args):
 	out = {'dbxref': d['dbxref']}
-	definition = {}
 	if args.basic:
-		if 'name' in d:
-			out['name'] = d['name']
-		if 'alternative_names' in d:
-			out['synonyms'] = d.pop('alternative_names')
-		if 'reaction_catalysed' in d:
-			definition['reaction_catalysed'] = d['reaction_catalysed']
-		if 'cofactors' in d:
-			definition['cofactors'] = d['cofactors']
-		if 'comments' in d:
-			definition['comments'] = d['comments']
-		if len(definition) == 1:
-			out['deifinition'] = definition[0]
-		elif len(definition) > 1:
-			out['deifinition'] = definition
-	if 'uniprot' in d and args.references:
+		out.update(read_basic(d))
+	if args.references:
+		out['uniprot'] = d['uniprot']
+	if not args.basic and not args.references:
+		out.update(read_basic(d))
 		out['uniprot'] = d['uniprot']
 	return (out)
 

scripts/retrieve_gene_ontology.py

@@ -26,17 +26,28 @@ def main():
 		d = json.loads(r.text)
 		output = {'dbxref': entry['dbxref']}
 		if args.basic:
-			output['definition'] = d['results'][0]['definition']['text']
-			output['name'] = d['results'][0]['name']
-			output['synonyms'] = d['results'][0]['synonyms']
+			output.update(read_basic(d))
 		if args.relations:
-			output['relations']= {'children': d['results'][0]['children']}
-			for child in output['relations']['children']:
-				child['type'] = child.pop('relation')
-			output['relations']['parent'] = parse_history(d['results'][0]['history'])
+			output.update(read_relations(d))
+		if not args.basic and not args.relations:
+			output.update(read_basic(d))
+			output.update(read_relations(d))
 		documents.append(output)
 	print (json.dumps(documents))
 
+def read_basic(d):
+	out = {'definition': d['results'][0]['definition']['text']}
+	out['name'] = d['results'][0]['name']
+	out['synonyms'] = d['results'][0]['synonyms']
+	return (out)
+
+def read_relations(d):
+	out = {'relations': {'children': d['results'][0]['children']}}
+	for child in out['relations']['children']:
+		child['type'] = child.pop('relation')
+	out['relations']['parents'] = parse_history(d['results'][0]['history'])
+	return (out)
+
 def parse_history(h):
 	out = []
 	for history in reversed(h):

scripts/retrieve_sequence_ontology.py

@@ -44,6 +44,9 @@ def main():
 			output.update(format_output(d))
 		if args.relations:
 			output['relations'] = resolve_relations(entry)
+		if 'id' in d and d['id'] == entry['dbxref'] and not args.basic and not args.relations:
+			output.update(format_output(d))
+			output['relations'] = resolve_relations(entry)
 		documents.append(output)
 	print (json.dumps(documents))
 
@@ -53,9 +56,9 @@ def resolve_relations(entry):
 	lines = r.text.strip().split('\n')
 	lines[0] = lines[0].split('\t')
 	lines[1] = lines[1].split('\t')
-	dic = {'parent': []}
+	dic = {'parents': []}
 	if lines[1][3] != '':
-		dic['parent'] = lines[1][3].split(',')
+		dic['parents'] = lines[1][3].split(',')
 	if len(lines[1]) == 5:
 	    dic['children'] = lines[1][4].split(',')
 	else:

scripts/tags.txt

 enzyme:
-"UniProtKB/Swiss-Prot":	[["", ""], ...]
-"dbxref":		""
-"definition":		{"cofactors": ["", ...], "comments": ["", ...], "reaction_catalysed": ["", ...]}
-"name":			""
-"synonyms":		["", ...]
+	"dbxref":				""
+	"definition":			{"cofactors": ["", ...], "comments": ["", ...], "reaction_catalysed": ["", ...]}
+	"name":					""
+	"synonyms":				["", ...]
+	"uniprot":				["", ...]
 
+--basic:
+	"dbxref":				""
+	"definition":			{"cofactors": ["", ...], "comments": ["", ...], "reaction_catalysed": ["", ...]}
+	"name":					""
+	"synonyms":				["", ...]
+
+--references:
+	"dbxref":				""
+	"uniprot":				["", ...]
+
+
+	
 gene ontology:
-"children":		[{"id": "", "relation": ""}, ...]
-"dbxref":		""
-"definition":		""
-"name":			""
-"synonyms":		[{"name": "", "type": ""}, ...]
+	"dbxref":				""
+	"definition":			""
+	"name":					""
+	"relations":			{"children": [{"id": "", "type": ""}, ...], "parents": [{"id": "", "type": ""}, ...]}
+	"synonyms":				[{"name": "", "type": ""}, ...]
+
+--basic:
+	"dbxref":				""
+	"definition":			""
+	"name":					""
+	"synonyms":				[{"name": "", "type": ""}, ...]
+
+--relations:
+	"dbxref":				""
+	"relations":			{"children": [{"id": "", "type": ""}, ...], "parents": [{"id": "", "type": ""}, ...]}
+
+
+
+pfam:
+	"dbxref":				""
+
+--basic:
+	"dbxref":				""
+
+--annotation:
+	"dbxref":				""
+
+
 
 sequence ontology:
-"dbxref":		""
-"definition":		""
-"name":			""
-"namespace":		""
-"parent":		""
-"synonyms":		[{"name": "", "type": ""}, ...]
+	"dbxref":				""
+	"definition":			""
+	"name":					""
+	"namespace":			""
+	"relations:				{"children": ["", ...], "parents": ["", ...]}
+	"synonyms":				[{"name": "", "type": ""}, ...]
+
+--basic:
+	"dbxref":				""
+	"definition":			""
+	"name":					""
+	"namespace":			""
+	"synonyms":				[{"name": "", "type": ""}, ...]
+
+--relations:
+	"dbxref":				""
+	"relations:				{"children": ["", ...], "parents": ["", ...]}
+
+
+
+uniprot:	
+	"acessions":			["", ...]
+	"alternative_names":	["", ...]	
+	"dbxref":				""
+	"dbxrefs":				["", ...]
+	"description":			""
+	"keywords":				["", ...]
+	"organism":				""
+	"recommended_name":		{"full": ""}
+	"sequence":				""
+
+--basic:
+	"dbxref":				""
+	"description":			""
+
+--sequence:
+	"dbxref":				""
+	"sequence":				""
+
+--organism:
+	"dbxref":				""
+	"organism":				""
+
+--annotation:
+	"acessions":			["", ...]
+	"alternative_names":	["", ...]	
+	"dbxref":				""
+	"dbxrefs":				["", ...]
+	"keywords":				["", ...]
+	"recommended_name":		{"full": ""}
+
+--features:
+	"dbxref":				""