Error in antismash_overview : invalid literal "<" for int in start position of region field

[OmkarSaMo]

The following issue appears in quite a few cases while running rule antismash_overview.

INFO     23/01 12:22:39   Getting antismash regions from record: JAPENF010000002
INFO     23/01 12:22:39   Grabbing information from region 1.1
Traceback (most recent call last):
  File "/datadrive/data3/g1115-paper/workflow/bgcflow/bgcflow/data/get_antismash_overview.py", line 128, in <module>
    get_antismash_overview(sys.argv[1], sys.argv[2], sys.argv[3])
  File "/datadrive/data3/g1115-paper/workflow/bgcflow/bgcflow/data/get_antismash_overview.py", line 110, in get_antismash_overview
    output_cluster["region_length"] = int(output_cluster["end_pos"]) - int(
                                                                       ^^^^
ValueError: invalid literal for int() with base 10: '<0'

Here is the screenshot of the region filed in the antiSMASH results genbank file. The location is <1..32213 which is causing the issue.

@SJShaw - is it normal that the region field location of antiSMASH genbank file starts with "<" in few cases instead of a number?

     region          <1..32213
                     /candidate_cluster_numbers="1"
                     /candidate_cluster_numbers="2"
                     /contig_edge="True"
                     /product="other"
                     /product="NRPS"
                     /region_number="1"
                     /rules="(LmbU or Neocarzinostat or fom1 or bcpB or frbD or
                     mitE or vlmB or prnB or CaiA or bacilysin or orf2_PTase)"
                     /rules="cds(Condensation and (AMP-binding or A-OX))"
                     /tool="antismash"

PFA Json file for recreating the issue
NBC_00340.zip

[SJShaw]

It's entirely normal if the first gene in the region has an inexact start position (BeforePosition). The same can be true for the end position and AfterPostion.

Don't attempt to parse a genbank location as if it's boring old ints, it'll bite you. Use the JSON and fetch the areas key for more machine readable data:
"areas": [{"start": 0, "end": 32213, "products": ["other"...
So for that JSON you attached:

import json
with open(json_file) as handle:
  data = json.load(handle)
for area in data["records"][0]["areas"]:
  print(area["start"], area["end"])

outputs:

0 32213
32980 106973
...

Use whatever JSON parser you like instead (like jq on the command line).