Retriever for Rfam

dbxref/retrieve/rfam.py

+#!/usr/bin/env python3
+
+import dbxref.resolver
+import requests
+import logging
+import json
+import argparse
+import xml.etree.ElementTree as ET
+
+logger = logging.getLogger(__name__)
+
+
+def main():
+    """main()method for script usage"""
+    parser = argparse.ArgumentParser(description="Retrieve Rfam json documents and parse them into dbxref json format")
+    parser.add_argument("--basics", "-b", action="store_true", help="Include basic informations such as dbxref_id, "
+                                                                    "name, description and comment.")
+    parser.add_argument("--references", "-r", action="store_true", help="Include reference information.")
+    parser.add_argument("dbxref", nargs=argparse.REMAINDER)
+    args = parser.parse_args()
+
+    if None not in (args.basics, args.references):
+        args.basics = True
+        args.references = True
+
+    dbxrefs = dbxref.resolver.convert_to_dbxrefs(args.dbxref)
+    documents = retrieve(dbxrefs, basics=args.basics, references=args.references)
+    print(json.dumps(documents, sort_keys=True, indent=4))
+
+
+def retrieve(dbxrefs, basics, references):
+    """Retrieve rfam json documents and parse into dbxref json format"""
+    resolved = dbxref.resolver.resolve(dbxrefs, check_existence=False)
+    documents = []
+    for entry in resolved:
+        # Construct URL for retrival
+        json_url = entry["locations"]["json"][0]
+        logger.debug("URL: %s", json_url)
+        r = requests.get(json_url)
+        logger.debug("Content: %s", r.text)
+        rfam = json.loads(r.text)
+        # Parse information
+        output = {}
+        if basics:
+            try:
+                output.update({"dbxref": rfam["rfam"]["acc"],
+                               "name": rfam["rfam"]["id"],
+                               "description": rfam["rfam"]["description"],
+                               "comment": rfam["rfam"]["comment"]
+                               })
+            except KeyError:
+                print("Basic information weren't fully or only partly available. "
+                      "Please check the dbxref and the Rfam-site.")
+        if references:
+            try:
+                output.update({"references": {"author": rfam["rfam"]["curation"]["author"],
+                                              "DOI": rfam["rfam"]["curation"]["structure_source"],
+                                              "type": rfam["rfam"]["curation"]["type"]
+                                              }
+                               })
+            except KeyError:
+                print("References weren't fully or only partly available. Please check the dbxref and the Rfam-site")
+        documents.append(output)
+
+    return documents
+
+
+if __name__ == "__main__":
+    main()