ssi-analysis-result-parsers 0.0.15__py3-none-any.whl → 0.0.16__py3-none-any.whl

ssi_analysis_result_parsers/Spyogenes_parser.py

@@ -131,7 +131,7 @@ def extract_emm_type(emm_blast_tsv: Path):
                     )
 
                 emm_typing_results["ENN_type"] = (
-                    "ENN" + blast_df_unique.iloc[1]["qseqid"][3:]
+                    "EMM" + blast_df_unique.iloc[1]["qseqid"][3:]
                 )
                 if (
                     blast_df_unique.iloc[1]["length"] < blast_df_unique.iloc[1]["qlen"]
@@ -148,7 +148,7 @@ def extract_emm_type(emm_blast_tsv: Path):
                     or emm_maintype in mrp_types_in_emm_plus_mrp_operons
                 ):
                     emm_typing_results["MRP_type"] = (
-                        "MRP" + emm_typing_results["EMM_type"][3:]
+                        "EMM" + emm_typing_results["EMM_type"][3:]
                     )
                     emm_typing_results["EMM_type"] = (
                         "EMM" + emm_typing_results["ENN_type"][3:]
@@ -158,7 +158,7 @@ def extract_emm_type(emm_blast_tsv: Path):
 
             elif blast_df_unique.shape[0] == 3:
                 emm_typing_results["MRP_type"] = (
-                    "MRP" + blast_df_unique.iloc[0]["qseqid"][3:]
+                    "EMM" + blast_df_unique.iloc[0]["qseqid"][3:]
                 )
                 if (
                     blast_df_unique.iloc[0]["length"] < blast_df_unique.iloc[0]["qlen"]
@@ -182,7 +182,7 @@ def extract_emm_type(emm_blast_tsv: Path):
                     )
 
                 emm_typing_results["ENN_type"] = (
-                    "ENN" + blast_df_unique.iloc[2]["qseqid"][3:]
+                    "EMM" + blast_df_unique.iloc[2]["qseqid"][3:]
                 )
                 if (
                     blast_df_unique.iloc[2]["length"] < blast_df_unique.iloc[2]["qlen"]
@@ -275,7 +275,7 @@ def Spyogenes_parser(
 ) -> None:
     """ """
     results = SpyogenesResults.from_tool_paths(
-        legionella_sbt_results_tsv=emm_blast_tsv, sample_name=sample_name
+        emm_blast_tsv=emm_blast_tsv, sample_name=sample_name
     )
     results.write_tsv(output_file=output_file)
 

{ssi_analysis_result_parsers-0.0.15.dist-info → ssi_analysis_result_parsers-0.0.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ssi_analysis_result_parsers
-Version: 0.0.15
+Version: 0.0.16
 Summary: TODO
 Home-page: https://github.com/thej-ssi/ssi_analysis_result_parsers
 Author: Thor Bech Johannesen

{ssi_analysis_result_parsers-0.0.15.dist-info → ssi_analysis_result_parsers-0.0.16.dist-info}/RECORD

@@ -2,7 +2,7 @@ ssi_analysis_result_parsers/Ecoli_parser.py,sha256=IQDbTPxvaQBf3el92_76QQ3prA2HG
 ssi_analysis_result_parsers/Hinfluenzae_parser.py,sha256=ch2pI1NEZPteewOXfeN8w4HW9Rhpr5ngdUIPwPqoA4Y,11876
 ssi_analysis_result_parsers/Legionella_parser.py,sha256=Yp14u8xqItrIb-uVk786K6jlIi-HNfn0wnQMo_R_X1c,6950
 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/Spyogenes_parser.py,sha256=X-orRLOaBWMnxkSRGBvEphD0Yfnrb9TVntAFXpa71VM,12718
 ssi_analysis_result_parsers/__init__.py,sha256=go20U3RCVaJ2N55RnX4tO5rinfUCRV0puFyrHCto8yw,23
 ssi_analysis_result_parsers/_modidx.py,sha256=odzq7igGyMkQ34NKL08Rr6qT7attmv2HhQPP6bwi51M,27684
 ssi_analysis_result_parsers/blast_parser.py,sha256=pIzMGk5-VyTy8uzFncTiIsy80wQxl9NbNiGI_K7XMaM,8658
@@ -11,7 +11,7 @@ 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-0.0.15.dist-info/licenses/LICENSE,sha256=p6aTb6QIfqyZ2Uux2VjV4F2zthdUSHZOjB4mfwGc7fo,1094
+ssi_analysis_result_parsers-0.0.16.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
@@ -54,8 +54,8 @@ 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-0.0.15.dist-info/METADATA,sha256=iVugrZ3dTgq1Ot87eUctd7bpHgNcC1-kPOC60Sl9TY0,2766
-ssi_analysis_result_parsers-0.0.15.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-ssi_analysis_result_parsers-0.0.15.dist-info/entry_points.txt,sha256=D-ZVsNLN5L6Hew4E1gyNc3sFsiBdswPPQsUpH3NAHnU,1109
-ssi_analysis_result_parsers-0.0.15.dist-info/top_level.txt,sha256=kVBbBavSQeQsoZCMoiur-3tQ_UT5CeO0L3PwjSdM2yQ,96
-ssi_analysis_result_parsers-0.0.15.dist-info/RECORD,,
+ssi_analysis_result_parsers-0.0.16.dist-info/METADATA,sha256=5Q-BDuAdWKu5OaULwySEVgMEpGZM0b4tK_5Lr4sSkOI,2766
+ssi_analysis_result_parsers-0.0.16.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+ssi_analysis_result_parsers-0.0.16.dist-info/entry_points.txt,sha256=D-ZVsNLN5L6Hew4E1gyNc3sFsiBdswPPQsUpH3NAHnU,1109
+ssi_analysis_result_parsers-0.0.16.dist-info/top_level.txt,sha256=kVBbBavSQeQsoZCMoiur-3tQ_UT5CeO0L3PwjSdM2yQ,96
+ssi_analysis_result_parsers-0.0.16.dist-info/RECORD,,