ssi-analysis-result-parsers 0.0.12__py3-none-any.whl → 0.0.14__py3-none-any.whl

ssi_analysis_result_parsers/Nmeningitidis_parser.py

@@ -41,18 +41,25 @@ def extract_meningotype(meningotype_tsv: Path):
     if meningotype_tsv.exists():
         try:
             df = pandas.read_csv(meningotype_tsv, sep="\t")
-            PorA_split = df["PorA"][0].split(",")
-            VR1 = PorA_split[0]
-            try:
-                VR2 = PorA_split[1]
-            except:
-                VR2 = ""
-            return {
-                "SEROGROUP": df["SEROGROUP"][0],
-                "VR1": VR1,
-                "VR2": VR2,
-                "FetA": df["FetA"][0],
-            }
+            if df.shape[0] > 0:
+                PorA_split = df.iloc[0]["PorA"].split(",")
+                VR1 = PorA_split[0]
+                try:
+                    VR2 = PorA_split[1]
+                except:
+                    VR2 = ""
+                return {
+                    "SEROGROUP": df.iloc[0]["SEROGROUP"],
+                    "VR1": VR1,
+                    "VR2": VR2,
+                    "FetA": df.iloc[0]["FetA"],
+                }
+            else:
+                print(
+                    f"Meningotype output file empty at {meningotype_tsv}",
+                    file=sys.stderr,
+                )
+                return None
         except pandas.errors.EmptyDataError:
             print(
                 f"Meningotype output file empty at {meningotype_tsv}", file=sys.stderr

ssi_analysis_result_parsers/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.11"
+__version__ = "0.0.13"

{ssi_analysis_result_parsers-0.0.12.dist-info → ssi_analysis_result_parsers-0.0.14.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ssi_analysis_result_parsers
-Version: 0.0.12
+Version: 0.0.14
 Summary: TODO
 Home-page: https://github.com/thej-ssi/ssi_analysis_result_parsers
 Author: Thor Bech Johannesen

{ssi_analysis_result_parsers-0.0.12.dist-info → ssi_analysis_result_parsers-0.0.14.dist-info}/RECORD

@@ -1,8 +1,8 @@
 ssi_analysis_result_parsers/Ecoli_parser.py,sha256=lKNnx27KqxpX3yv1RAP-sBATMGf9yjfSs4-d50mR2cA,22704
 ssi_analysis_result_parsers/Legionella_parser.py,sha256=Yp14u8xqItrIb-uVk786K6jlIi-HNfn0wnQMo_R_X1c,6950
-ssi_analysis_result_parsers/Nmeningitidis_parser.py,sha256=jLYCz9NSPLDt44YM60whEltTeY8jir6N1UVk4UhG85M,7016
+ssi_analysis_result_parsers/Nmeningitidis_parser.py,sha256=Jl1ubU2T6XbwffpglMBsvp3tOb5DAG72MbDnN6RB0qc,7310
 ssi_analysis_result_parsers/Spyogenes_parser.py,sha256=Cjibp7iKGofjSp-igm-jmjBVkQ6-zxYQWVSZT-Vx3Fo,12731
-ssi_analysis_result_parsers/__init__.py,sha256=OaIl7v-6zEWEY90Jlh6yoBjO3zWX1oX7RsvqrK3o1TU,23
+ssi_analysis_result_parsers/__init__.py,sha256=SxvRes_80c-42zwvn5BXPvpGVs_EZ69FUEtUBF1k9Ts,23
 ssi_analysis_result_parsers/_modidx.py,sha256=rrpJq1GcgPx34ag7bGe6VvBl4v-tC-ErTTvYAjHW7uI,22865
 ssi_analysis_result_parsers/blast_parser.py,sha256=pIzMGk5-VyTy8uzFncTiIsy80wQxl9NbNiGI_K7XMaM,8658
 ssi_analysis_result_parsers/core.py,sha256=8CzFMDrGJ24D9aoIebLsG8tx-OxvYJod1cxBITqNfaY,12258
@@ -10,7 +10,7 @@ ssi_analysis_result_parsers/hello_world.py,sha256=jpN94sqYuNHqUbUZMCJ35qGY5iLPB_
 ssi_analysis_result_parsers/some_string.py,sha256=JwmAXKbX_JgY8UGh4FAu5-7ZjezcAEhq4Q2B73pWp2M,923
 ssi_analysis_result_parsers/config/config.default.env,sha256=Zt6bfPbVV3rYCksoebX1ruAdFgeD9wqAnKDtswhtJJM,1390
 ssi_analysis_result_parsers/config/config.default.yaml,sha256=3qgUrUtQpxrzYv7WQaHsvz9dQB0RALKNU0idxv7oRqM,460
-ssi_analysis_result_parsers-0.0.12.dist-info/licenses/LICENSE,sha256=p6aTb6QIfqyZ2Uux2VjV4F2zthdUSHZOjB4mfwGc7fo,1094
+ssi_analysis_result_parsers-0.0.14.dist-info/licenses/LICENSE,sha256=p6aTb6QIfqyZ2Uux2VjV4F2zthdUSHZOjB4mfwGc7fo,1094
 test_input/.DS_Store,sha256=sdTEvl9DTKPHNPYYjMqDepX7q7ZETlonk21tGEuWLao,6148
 test_input/empty_file.txt,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 test_input/Ecoli/ERR14229029.res,sha256=AmVZwbiUTjOQLe7SmSKWt9-URdcrsLSxt9hHUh-nFUY,129
@@ -46,8 +46,8 @@ test_output/output_with_sample_name.tsv,sha256=NQG7WaxczuWCCsX2a9MUxCCYpbuAirz9g
 test_output/test.tsv,sha256=6DGzarXMkUP03Z58vZimc-gu1K2k84zxZLWWF2HROCg,277
 test_output/test_batch_output.tsv,sha256=6DGzarXMkUP03Z58vZimc-gu1K2k84zxZLWWF2HROCg,277
 test_output/Ecoli/KMA_cases_parser.tsv,sha256=Wf3JkSppRN5AK2zRJmFQlwVfCMyJfgyyBpTjb1sK6Uw,586
-ssi_analysis_result_parsers-0.0.12.dist-info/METADATA,sha256=7gLCEO8s0y9sleizoV_yWq7pZi5WQCNrO6IUOCj-uSE,2766
-ssi_analysis_result_parsers-0.0.12.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-ssi_analysis_result_parsers-0.0.12.dist-info/entry_points.txt,sha256=OixZpyfeqGO7S_8k1ExmGc32EFBt9RX6C1W3H8vZ1K4,913
-ssi_analysis_result_parsers-0.0.12.dist-info/top_level.txt,sha256=kVBbBavSQeQsoZCMoiur-3tQ_UT5CeO0L3PwjSdM2yQ,96
-ssi_analysis_result_parsers-0.0.12.dist-info/RECORD,,
+ssi_analysis_result_parsers-0.0.14.dist-info/METADATA,sha256=et7Zc4tL-fB7wsPhc1HylmjmqOa-1zPEmI7_VCYSNZU,2766
+ssi_analysis_result_parsers-0.0.14.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+ssi_analysis_result_parsers-0.0.14.dist-info/entry_points.txt,sha256=OixZpyfeqGO7S_8k1ExmGc32EFBt9RX6C1W3H8vZ1K4,913
+ssi_analysis_result_parsers-0.0.14.dist-info/top_level.txt,sha256=kVBbBavSQeQsoZCMoiur-3tQ_UT5CeO0L3PwjSdM2yQ,96
+ssi_analysis_result_parsers-0.0.14.dist-info/RECORD,,