Added options for deoverlap file name and fixed old json entry lookup

helpers/database-import-scripts/rnacentral/generate_rnacentral_json.py

@@ -59,9 +59,9 @@ def main(rfam_info, metadata, outfile, deoverlap_dir, gff_dir, fasta_dir, previo
  # Check which entries are different in this version and bump the version in the json
  for index, new_entry in enumerate(json_data):
  if new_entry["primaryId"] in previous_primary_ids:
- old_entry = get_entry(previous_json_data, json_data[0]["primaryId"], "data")
- new_entry = get_entry(json_data, json_data[0]["primaryId"], None)
- if old_entry is not None and old_entry != new_entry:
+ old_entry = get_entry(previous_json_data, json_data[index]["primaryId"], "data")
+ new_entry = get_entry(json_data, json_data[index]["primaryId"], None)
+ if old_entry != new_entry:
  json_data = up_the_version(json_data, index, old_entry["version"])
  final_dict["data"].extend(json_data)
  final_dict["metaData"] = metadata_json
@@ -174,9 +174,12 @@ def generate_data_dict(mgnify_accession, sample_accession, taxonomy, deoverlap_d
  global SKIP_CMSCAN, SKIP_GFF, GOOD, BAD_SEQUENCE
  deoverlap_path = os.path.join(deoverlap_dir, "{}.cmscan-deoverlap.tbl".format(mgnify_accession))
  if not os.path.exists(deoverlap_path):
- logging.warning("cmscan file for accession {} doesn't exist. Skipping.".format(mgnify_accession))
- SKIP_CMSCAN += 1
- return None
+ # check if the naming has changed
+ deoverlap_path = os.path.join(deoverlap_dir, "{}.ncrna.deoverlap.tbl".format(mgnify_accession))
+ if not os.path.exists(deoverlap_path):
+ logging.warning("cmscan file for accession {} doesn't exist. Skipping.".format(mgnify_accession))
+ SKIP_CMSCAN += 1
+ return None
  try:
  gff_path = glob.glob(os.path.join(gff_dir, mgnify_accession + ".*"))[0]
  except:
@@ -375,7 +378,7 @@ def get_publications(genome_sample_accession, reported_project, insdc_accession)
  logging.error("Biosample could not be obtained for an ENA genome {}".
  format(insdc_accession))
  sys.exit("ERROR: cannot proceed because at least one ENA sample is not found in ENA.")
- return list(filter(None, list(set(publications))))
+ return sorted(list(filter(None, list(set(publications)))))
 
 
 def identify_derived_sample_issue(ena_data):