ssi-analysis-result-parsers 0.0.15__py3-none-any.whl → 0.0.17__py3-none-any.whl

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Files changed (8) hide show
  1. ssi_analysis_result_parsers/Spyogenes_parser.py +6 -5
  2. ssi_analysis_result_parsers/__init__.py +1 -1
  3. {ssi_analysis_result_parsers-0.0.15.dist-info → ssi_analysis_result_parsers-0.0.17.dist-info}/METADATA +1 -1
  4. {ssi_analysis_result_parsers-0.0.15.dist-info → ssi_analysis_result_parsers-0.0.17.dist-info}/RECORD +8 -8
  5. {ssi_analysis_result_parsers-0.0.15.dist-info → ssi_analysis_result_parsers-0.0.17.dist-info}/WHEEL +0 -0
  6. {ssi_analysis_result_parsers-0.0.15.dist-info → ssi_analysis_result_parsers-0.0.17.dist-info}/entry_points.txt +0 -0
  7. {ssi_analysis_result_parsers-0.0.15.dist-info → ssi_analysis_result_parsers-0.0.17.dist-info}/licenses/LICENSE +0 -0
  8. {ssi_analysis_result_parsers-0.0.15.dist-info → ssi_analysis_result_parsers-0.0.17.dist-info}/top_level.txt +0 -0
ssi_analysis_result_parsers/Spyogenes_parser.py CHANGED
@@ -87,6 +87,7 @@ def extract_emm_type(emm_blast_tsv: Path):
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  round((blast_df["sstart"] - blast_df["qstart"] + 1) / 100),
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  round((blast_df["send"] - blast_df["qstart"] + 1) / 100),
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  )
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+ blast_df = blast_df.query("bitscore > 200")
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  blast_df_unique = (
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  blast_df.sort_values(by=["bitscore"], ascending=False)
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  .groupby("extended_sstart")
@@ -131,7 +132,7 @@ def extract_emm_type(emm_blast_tsv: Path):
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  )
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  emm_typing_results["ENN_type"] = (
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- "ENN" + blast_df_unique.iloc[1]["qseqid"][3:]
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+ "EMM" + blast_df_unique.iloc[1]["qseqid"][3:]
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  )
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  if (
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  blast_df_unique.iloc[1]["length"] < blast_df_unique.iloc[1]["qlen"]
@@ -148,7 +149,7 @@ def extract_emm_type(emm_blast_tsv: Path):
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  or emm_maintype in mrp_types_in_emm_plus_mrp_operons
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  ):
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  emm_typing_results["MRP_type"] = (
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- "MRP" + emm_typing_results["EMM_type"][3:]
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+ "EMM" + emm_typing_results["EMM_type"][3:]
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  )
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  emm_typing_results["EMM_type"] = (
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  "EMM" + emm_typing_results["ENN_type"][3:]
@@ -158,7 +159,7 @@ def extract_emm_type(emm_blast_tsv: Path):
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  elif blast_df_unique.shape[0] == 3:
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  emm_typing_results["MRP_type"] = (
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- "MRP" + blast_df_unique.iloc[0]["qseqid"][3:]
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+ "EMM" + blast_df_unique.iloc[0]["qseqid"][3:]
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  )
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  if (
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  blast_df_unique.iloc[0]["length"] < blast_df_unique.iloc[0]["qlen"]
@@ -182,7 +183,7 @@ def extract_emm_type(emm_blast_tsv: Path):
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  )
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  emm_typing_results["ENN_type"] = (
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- "ENN" + blast_df_unique.iloc[2]["qseqid"][3:]
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+ "EMM" + blast_df_unique.iloc[2]["qseqid"][3:]
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  )
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  if (
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  blast_df_unique.iloc[2]["length"] < blast_df_unique.iloc[2]["qlen"]
@@ -275,7 +276,7 @@ def Spyogenes_parser(
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  ) -> None:
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  """ """
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  results = SpyogenesResults.from_tool_paths(
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- legionella_sbt_results_tsv=emm_blast_tsv, sample_name=sample_name
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+ emm_blast_tsv=emm_blast_tsv, sample_name=sample_name
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  )
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  results.write_tsv(output_file=output_file)
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ssi_analysis_result_parsers/__init__.py CHANGED
@@ -1 +1 @@
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- __version__ = "0.0.15"
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+ __version__ = "0.0.16"
{ssi_analysis_result_parsers-0.0.15.dist-info → ssi_analysis_result_parsers-0.0.17.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: ssi_analysis_result_parsers
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- Version: 0.0.15
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+ Version: 0.0.17
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  Summary: TODO
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  Home-page: https://github.com/thej-ssi/ssi_analysis_result_parsers
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  Author: Thor Bech Johannesen
{ssi_analysis_result_parsers-0.0.15.dist-info → ssi_analysis_result_parsers-0.0.17.dist-info}/RECORD RENAMED
@@ -2,8 +2,8 @@ ssi_analysis_result_parsers/Ecoli_parser.py,sha256=IQDbTPxvaQBf3el92_76QQ3prA2HG
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  ssi_analysis_result_parsers/Hinfluenzae_parser.py,sha256=ch2pI1NEZPteewOXfeN8w4HW9Rhpr5ngdUIPwPqoA4Y,11876
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  ssi_analysis_result_parsers/Legionella_parser.py,sha256=Yp14u8xqItrIb-uVk786K6jlIi-HNfn0wnQMo_R_X1c,6950
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  ssi_analysis_result_parsers/Nmeningitidis_parser.py,sha256=Jl1ubU2T6XbwffpglMBsvp3tOb5DAG72MbDnN6RB0qc,7310
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- ssi_analysis_result_parsers/Spyogenes_parser.py,sha256=Cjibp7iKGofjSp-igm-jmjBVkQ6-zxYQWVSZT-Vx3Fo,12731
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- ssi_analysis_result_parsers/__init__.py,sha256=go20U3RCVaJ2N55RnX4tO5rinfUCRV0puFyrHCto8yw,23
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+ ssi_analysis_result_parsers/Spyogenes_parser.py,sha256=mVxfAxEIzWsO11rJjUftIaxTh5oD4U046rd11E_5uCQ,12766
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+ ssi_analysis_result_parsers/__init__.py,sha256=8ss7zPyQ3YfaQJw9IIGX35NOL7ASZ7-LErAxKnQDN7c,23
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  ssi_analysis_result_parsers/_modidx.py,sha256=odzq7igGyMkQ34NKL08Rr6qT7attmv2HhQPP6bwi51M,27684
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  ssi_analysis_result_parsers/blast_parser.py,sha256=pIzMGk5-VyTy8uzFncTiIsy80wQxl9NbNiGI_K7XMaM,8658
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  ssi_analysis_result_parsers/core.py,sha256=8CzFMDrGJ24D9aoIebLsG8tx-OxvYJod1cxBITqNfaY,12258
@@ -11,7 +11,7 @@ ssi_analysis_result_parsers/hello_world.py,sha256=jpN94sqYuNHqUbUZMCJ35qGY5iLPB_
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  ssi_analysis_result_parsers/some_string.py,sha256=JwmAXKbX_JgY8UGh4FAu5-7ZjezcAEhq4Q2B73pWp2M,923
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  ssi_analysis_result_parsers/config/config.default.env,sha256=Zt6bfPbVV3rYCksoebX1ruAdFgeD9wqAnKDtswhtJJM,1390
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  ssi_analysis_result_parsers/config/config.default.yaml,sha256=3qgUrUtQpxrzYv7WQaHsvz9dQB0RALKNU0idxv7oRqM,460
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- ssi_analysis_result_parsers-0.0.15.dist-info/licenses/LICENSE,sha256=p6aTb6QIfqyZ2Uux2VjV4F2zthdUSHZOjB4mfwGc7fo,1094
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+ ssi_analysis_result_parsers-0.0.17.dist-info/licenses/LICENSE,sha256=p6aTb6QIfqyZ2Uux2VjV4F2zthdUSHZOjB4mfwGc7fo,1094
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  test_input/.DS_Store,sha256=sdTEvl9DTKPHNPYYjMqDepX7q7ZETlonk21tGEuWLao,6148
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  test_input/empty_file.txt,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  test_input/Ecoli/ERR14229029.res,sha256=AmVZwbiUTjOQLe7SmSKWt9-URdcrsLSxt9hHUh-nFUY,129
@@ -54,8 +54,8 @@ test_output/output_with_sample_name.tsv,sha256=NQG7WaxczuWCCsX2a9MUxCCYpbuAirz9g
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  test_output/test.tsv,sha256=6DGzarXMkUP03Z58vZimc-gu1K2k84zxZLWWF2HROCg,277
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  test_output/test_batch_output.tsv,sha256=6DGzarXMkUP03Z58vZimc-gu1K2k84zxZLWWF2HROCg,277
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  test_output/Ecoli/KMA_cases_parser.tsv,sha256=Wf3JkSppRN5AK2zRJmFQlwVfCMyJfgyyBpTjb1sK6Uw,586
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- ssi_analysis_result_parsers-0.0.15.dist-info/METADATA,sha256=iVugrZ3dTgq1Ot87eUctd7bpHgNcC1-kPOC60Sl9TY0,2766
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- ssi_analysis_result_parsers-0.0.15.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
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- ssi_analysis_result_parsers-0.0.15.dist-info/entry_points.txt,sha256=D-ZVsNLN5L6Hew4E1gyNc3sFsiBdswPPQsUpH3NAHnU,1109
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- ssi_analysis_result_parsers-0.0.15.dist-info/top_level.txt,sha256=kVBbBavSQeQsoZCMoiur-3tQ_UT5CeO0L3PwjSdM2yQ,96
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- ssi_analysis_result_parsers-0.0.15.dist-info/RECORD,,
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+ ssi_analysis_result_parsers-0.0.17.dist-info/METADATA,sha256=NQ3QR_55gMH8kUTr1NjeF5y9sRdTUQJKQ7BD6mpgHss,2766
58
+ ssi_analysis_result_parsers-0.0.17.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
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+ ssi_analysis_result_parsers-0.0.17.dist-info/entry_points.txt,sha256=D-ZVsNLN5L6Hew4E1gyNc3sFsiBdswPPQsUpH3NAHnU,1109
60
+ ssi_analysis_result_parsers-0.0.17.dist-info/top_level.txt,sha256=kVBbBavSQeQsoZCMoiur-3tQ_UT5CeO0L3PwjSdM2yQ,96
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+ ssi_analysis_result_parsers-0.0.17.dist-info/RECORD,,