added option to save output in json format

BIONF · Oct 24, 2023 · 7b003fa · 7b003fa
1 parent 60220b6
commit 7b003fa
Show file tree

Hide file tree

Showing 4 changed files with 25 additions and 3 deletions.
diff --git a/greedyFAS/calcFAS.py b/greedyFAS/calcFAS.py
@@ -107,6 +107,8 @@ def get_options():
     outargs.add_argument("--tsv", dest="tsv", action="store_true",
                          help="deactivates creation of the tsv output, either use together with --raw or "
                               "--phyloprofile")
+    outargs.add_argument("--json", dest="json", action="store_true",
+                         help="create json output")
     outargs.add_argument("--phyloprofile", dest="phyloprofile", default=None, type=str,
                          help="activate phyloprofile output, needs mapping file for all query proteins")
     outargs.add_argument("--domain", dest="domain", action="store_false",
@@ -178,7 +180,7 @@ def fas(args, toolpath):
                    "max_cardinality": args.max_cardinality, "cores": int(args.cpus), "raw": args.raw,
                    "bidirectional": args.bidirectional, "max_overlap": args.max_overlap,
                    "timelimit": args.timelimit, "phyloprofile": args.phyloprofile, "score_weights": [],
-                    "tsv": args.tsv, "max_overlap_percentage": 0.0, "domain": args.domain, "pairwise": None,
+                    "tsv": args.tsv, "json": args.json, "max_overlap_percentage": 0.0, "domain": args.domain, "pairwise": None,
                     "eInstance": args.eInstance, "eFeature": args.eFeature, "progress": True,
                     "empty_as_1": args.empty_as_1
                    }

diff --git a/greedyFAS/mainFAS/fasOutput.py b/greedyFAS/mainFAS/fasOutput.py
@@ -22,6 +22,7 @@
 
 
 from os.path import abspath
+import json
 
 
 def write_tsv_out(outpath, bidirectional, results):
@@ -45,6 +46,21 @@ def write_tsv_out(outpath, bidirectional, results):
     out.close()
 
 
+def write_json_out(outpath, bidirectional, results):
+    outdict = {}
+    for result in results[0]:
+        outdict[result[0], result[1]] = (result[2], ('NA', 'NA', 'NA', 'NA', 'NA'), result[3])
+    if bidirectional:
+        for result in results[1]:
+            outdict[result[1], result[0]] = (outdict[result[1], result[0]][0], result[2], outdict[result[1],
+                                                                                                  result[0]][2])
+    json_dict = {}
+    for pair in outdict:
+        json_dict['_'.join(pair)] = [f'{outdict[pair][0][0]:.4}', f'{outdict[pair][1][0]:.4}']
+    with open(f'{outpath}.json', 'w') as fp:
+        json.dump(json_dict, fp, ensure_ascii=False)
+
+
 def write_domain_out_fad(seed_proteome, query_proteome, seed, query, weights, scale, seedpath, querypath, out, option,
                          interprokeys, phmm):
     tools = option['input_linearized'] + option['input_normal']

diff --git a/greedyFAS/mainFAS/greedyFAS.py b/greedyFAS/mainFAS/greedyFAS.py
@@ -32,7 +32,7 @@
 from greedyFAS.mainFAS.fasInput import read_json
 from greedyFAS.mainFAS.fasInput import check_version
 from greedyFAS.mainFAS.fasOutput import write_domain_out
-from greedyFAS.mainFAS.fasOutput import write_tsv_out
+from greedyFAS.mainFAS.fasOutput import write_tsv_out, write_json_out
 from greedyFAS.mainFAS.fasOutput import phyloprofile_out
 from greedyFAS.mainFAS.fasScoring import sf_calc_score
 from greedyFAS.mainFAS.fasScoring import sf_entire_calc_score
@@ -152,11 +152,15 @@ def fc_start(option):
             phyloprofile_out(option["outpath"], True, option["phyloprofile"], (f_results, r_results))
         if not option['tsv']:
             write_tsv_out(option["outpath"], True, (f_results, r_results))
+        if option['json']:
+            write_json_out(option["outpath"], True, (f_results, r_results))
     else:
         print("calculating forward scores...")
         results = fc_main(domain_count, seed_proteome, query_proteome, clan_dict, option, interprokeys, phmm)
         if not option["tsv"]:
             write_tsv_out(option["outpath"], False, (results, None))
+        if option["json"]:
+            write_json_out(option["outpath"], False, (results, None))
         if option["phyloprofile"]:
             phyloprofile_out(option["outpath"], False, option["phyloprofile"], [results, None])
 

diff --git a/setup.py b/setup.py
@@ -28,7 +28,7 @@
 
 setup(
     name='greedyFAS',
-    version='1.17.13',
+    version='1.17.14',
     python_requires='>=3.7.0',
     description='A tool to compare protein feature architectures',
     long_description=long_description,