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json output #88

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10 changes: 10 additions & 0 deletions bin/ANARCI
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Original file line number Diff line number Diff line change
Expand Up @@ -100,6 +100,7 @@ if __name__ == "__main__":
parser.add_argument( '--restrict','-r', type=str, nargs="+", choices=["ig","tr","heavy", "light", "H", "K", "L", "A", "B"], default=False, help="Restrict ANARCI to only recognise certain types of receptor chains.", dest="restrict")
parser.add_argument( '--csv', action='store_true', default=False, help="Write the output in csv format. Outfile must be specified. A csv file is written for each chain type <outfile>_<chain_type>.csv. Kappa and lambda are considered together.", dest="csv")
parser.add_argument( '--outfile_hits','-ht', type=str, default=False, help="Output file for domain hit tables for each sequence. Otherwise not output.", dest="hitfile")
parser.add_argument('--json_output_hits', "-jht", type=str, help="Output file for domain hit tables for each sequence. Otherwise not output.", dest="json_hitfile")
parser.add_argument( '--hmmerpath','-hp', type=str, default="", help="The path to the directory containing hmmer programs. (including hmmscan)", dest="hmmerpath")
parser.add_argument( '--ncpu','-p', type=int, default=1, help="Number of parallel processes to use. Default is 1.", dest="ncpu")
parser.add_argument( '--assign_germline', action = 'store_true', default=False, help="Assign the v and j germlines to the sequence. The most sequence identical germline is assigned.", dest="assign_germline")
Expand Down Expand Up @@ -195,6 +196,15 @@ if __name__ == "__main__":
for line in hit_tables[i]:
print(" ".join( [ str(_).rjust(pad) for _ in line ]), file=outfile)
print("//", file=outfile)
if args.json_hitfile:
import json
hit_dicts = []
for table in hit_tables:
keys = table[0]
for row in table[1:]:
hit_dicts.append(dict(zip(keys, row)))
with open(args.json_hitfile, "w") as outfile:
json.dump(hit_dicts, outfile)
except Exception as e:
# An error occurred. Report to screen and die gracefully.
print("Error: ", e, file=sys.stderr)
Expand Down