ssi-analysis-result-parsers 0.0.7__tar.gz → 0.0.9__tar.gz

{ssi_analysis_result_parsers-0.0.7/ssi_analysis_result_parsers.egg-info → ssi_analysis_result_parsers-0.0.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ssi_analysis_result_parsers
-Version: 0.0.7
+Version: 0.0.9
 Summary: TODO
 Home-page: https://github.com/thej-ssi/ssi_analysis_result_parsers
 Author: Thor Bech Johannesen

{ssi_analysis_result_parsers-0.0.7 → ssi_analysis_result_parsers-0.0.9}/settings.ini

@@ -5,7 +5,7 @@
 ### Python library ###
 repo = ssi_analysis_result_parsers
 lib_name = %(repo)s
-version = 0.0.7
+version = 0.0.9
 min_python = 3.9
 license = MIT
 black_formatting = True

{ssi_analysis_result_parsers-0.0.7 → ssi_analysis_result_parsers-0.0.9}/ssi_analysis_result_parsers/Spyogenes_parser.py

@@ -56,7 +56,14 @@ def extract_emm_type(emm_blast_tsv: Path):
     """
 
     emm_types_in_emm_plus_mrp_operons = []  ### to update
-    mrp_types_in_emm_plus_mrp_operons = ["156"]  ### to update
+    mrp_types_in_emm_plus_mrp_operons = [
+        "134",
+        "156",
+        "159",
+        "164",
+        "174",
+        "205",
+    ]  ### to update
     emm_blast_tsv = Path(emm_blast_tsv)
     emm_typing_results = {"EMM_type": "-", "ENN_type": "-", "MRP_type": "-"}
     if not emm_blast_tsv.exists():
@@ -85,87 +92,119 @@ def extract_emm_type(emm_blast_tsv: Path):
         .groupby("extended_sstart")
         .first()
     )
-    if blast_df_unique.shape[0] == 1:
-        emm_typing_results["EMM_type"] = blast_df_unique.iloc[0]["qseqid"][3:]
-        if (
-            blast_df_unique.iloc[0]["length"] < 180
-            or blast_df_unique.iloc[0]["pident"] < 100
-        ):
-            emm_typing_results["EMM_type"] += "*"
-            notes.append(
-                f"EMM{blast_df_unique.iloc[0]['qseqid'][3:]} with {round(blast_df_unique.iloc[0]['pident'],2)} and length {blast_df_unique.iloc[0]['length']}/{blast_df_unique.iloc[0]['qlen']}"
-            )
-    else:
-        if blast_df_unique.iloc[0]["sstart"] < blast_df_unique.iloc[0]["send"]:
-            blast_df_unique = blast_df_unique.sort_values(by=["sstart"], ascending=True)
-        else:
-            blast_df_unique = blast_df_unique.sort_values(
-                by=["sstart"], ascending=False
+
+    if blast_df_unique.shape[0] == 0:
+        notes.append("No blast hits found for EMM genes")
+    elif len(set(blast_df_unique["sseqid"])) == 1:
+        if blast_df_unique.shape[0] == 1:
+            emm_typing_results["EMM_type"] = (
+                "EMM" + blast_df_unique.iloc[0]["qseqid"][3:]
             )
-        if blast_df_unique.shape[0] == 2:
-            emm_typing_results["EMM_type"] = blast_df_unique.iloc[0]["qseqid"][3:]
             if (
-                blast_df_unique.iloc[0]["length"] < 180
+                blast_df_unique.iloc[0]["length"] < blast_df_unique.iloc[0]["qlen"]
                 or blast_df_unique.iloc[0]["pident"] < 100
             ):
                 emm_typing_results["EMM_type"] += "*"
                 notes.append(
-                    f"EMM{blast_df_unique.iloc[0]['qseqid'][3:]} with pident {round(blast_df_unique.iloc[0]['pident'],2)} and length {blast_df_unique.iloc[0]['length']}/{blast_df_unique.iloc[0]['qlen']}"
+                    f"EMM{blast_df_unique.iloc[0]['qseqid'][3:]} with {round(blast_df_unique.iloc[0]['pident'],2)} and length {blast_df_unique.iloc[0]['length']}/{blast_df_unique.iloc[0]['qlen']}"
+                )
+        else:
+            if blast_df_unique.iloc[0]["sstart"] < blast_df_unique.iloc[0]["send"]:
+                blast_df_unique = blast_df_unique.sort_values(
+                    by=["sstart"], ascending=True
                 )
+            else:
+                blast_df_unique = blast_df_unique.sort_values(
+                    by=["sstart"], ascending=False
+                )
+            if blast_df_unique.shape[0] == 2:
+                emm_typing_results["EMM_type"] = (
+                    "EMM" + blast_df_unique.iloc[0]["qseqid"][3:]
+                )
+                if (
+                    blast_df_unique.iloc[0]["length"] < blast_df_unique.iloc[0]["qlen"]
+                    or blast_df_unique.iloc[0]["pident"] < 100
+                ):
+                    emm_typing_results["EMM_type"] += "*"
+                    notes.append(
+                        f"EMM{blast_df_unique.iloc[0]['qseqid'][3:]} with pident {round(blast_df_unique.iloc[0]['pident'],2)} and length {blast_df_unique.iloc[0]['length']}/{blast_df_unique.iloc[0]['qlen']}"
+                    )
 
-            emm_typing_results["ENN_type"] = blast_df_unique.iloc[1]["qseqid"][3:]
-            if (
-                blast_df_unique.iloc[1]["length"] < 180
-                or blast_df_unique.iloc[1]["pident"] < 100
-            ):
-                emm_typing_results["ENN_type"] += "*"
-                notes.append(
-                    f"ENN{blast_df_unique.iloc[1]['qseqid'][3:]} with pident {round(blast_df_unique.iloc[1]['pident'],2)} and length {blast_df_unique.iloc[1]['length']}/{blast_df_unique.iloc[1]['qlen']}"
+                emm_typing_results["ENN_type"] = (
+                    "ENN" + blast_df_unique.iloc[1]["qseqid"][3:]
                 )
+                if (
+                    blast_df_unique.iloc[1]["length"] < blast_df_unique.iloc[1]["qlen"]
+                    or blast_df_unique.iloc[1]["pident"] < 100
+                ):
+                    emm_typing_results["ENN_type"] += "*"
+                    notes.append(
+                        f"ENN{blast_df_unique.iloc[1]['qseqid'][3:]} with pident {round(blast_df_unique.iloc[1]['pident'],2)} and length {blast_df_unique.iloc[1]['length']}/{blast_df_unique.iloc[1]['qlen']}"
+                    )
+                emm_maintype = blast_df_unique.iloc[0]["qseqid"][3:].split(".")[0]
+                mrp_maintype = blast_df_unique.iloc[1]["qseqid"][3:].split(".")[0]
+                if (
+                    mrp_maintype in emm_types_in_emm_plus_mrp_operons
+                    or emm_maintype in mrp_types_in_emm_plus_mrp_operons
+                ):
+                    emm_typing_results["MRP_type"] = (
+                        "MRP" + emm_typing_results["EMM_type"][3:]
+                    )
+                    emm_typing_results["EMM_type"] = (
+                        "EMM" + emm_typing_results["ENN_type"][3:]
+                    )
+                    emm_typing_results["ENN_type"] = "-"
+                    notes.append(f"EMM redesignated due to known MRP+EMM operon")
 
-        emm_maintype = blast_df_unique.iloc[0]["qseqid"][3:].split(".")[0]
-        mrp_maintype = blast_df_unique.iloc[1]["qseqid"][3:].split(".")[0]
-        if (
-            mrp_maintype in emm_types_in_emm_plus_mrp_operons
-            or emm_maintype in mrp_types_in_emm_plus_mrp_operons
-        ):
-            emm_typing_results["MRP_type"] = emm_typing_results["EMM_type"]
-            emm_typing_results["EMM_type"] = emm_typing_results["ENN_type"]
-            emm_typing_results["ENN_type"] = "-"
-            notes.append(f"EMM redesignated due to known MRP+EMM operon")
-
-        elif blast_df_unique.shape[0] == 3:
-            emm_typing_results["MRP_type"] = blast_df_unique.iloc[0]["qseqid"][3:]
-            if (
-                blast_df_unique.iloc[0]["length"] < 180
-                or blast_df_unique.iloc[0]["pident"] < 100
-            ):
-                emm_typing_results["MRP_type"] += "*"
-                notes.append(
-                    f"MRP{blast_df_unique.iloc[0]['qseqid'][3:]} with pident {round(blast_df_unique.iloc[0]['pident'],2)} and length {blast_df_unique.iloc[0]['length']}/{blast_df_unique.iloc[0]['qlen']}"
+            elif blast_df_unique.shape[0] == 3:
+                emm_typing_results["MRP_type"] = (
+                    "MRP" + blast_df_unique.iloc[0]["qseqid"][3:]
                 )
+                if (
+                    blast_df_unique.iloc[0]["length"] < blast_df_unique.iloc[0]["qlen"]
+                    or blast_df_unique.iloc[0]["pident"] < 100
+                ):
+                    emm_typing_results["MRP_type"] += "*"
+                    notes.append(
+                        f"MRP{blast_df_unique.iloc[0]['qseqid'][3:]} with pident {round(blast_df_unique.iloc[0]['pident'],2)} and length {blast_df_unique.iloc[0]['length']}/{blast_df_unique.iloc[0]['qlen']}"
+                    )
 
-            emm_typing_results["EMM_type"] = blast_df_unique.iloc[1]["qseqid"][3:]
-            if (
-                blast_df_unique.iloc[1]["length"] < 180
-                or blast_df_unique.iloc[1]["pident"] < 100
-            ):
-                emm_typing_results["EMM_type"] += "*"
-                notes.append(
-                    f"EMM{blast_df_unique.iloc[1]['qseqid'][3:]} with pident {round(blast_df_unique.iloc[1]['pident'],2)} and length {blast_df_unique.iloc[1]['length']}/{blast_df_unique.iloc[1]['qlen']}"
+                emm_typing_results["EMM_type"] = (
+                    "EMM" + blast_df_unique.iloc[1]["qseqid"][3:]
                 )
+                if (
+                    blast_df_unique.iloc[1]["length"] < blast_df_unique.iloc[1]["qlen"]
+                    or blast_df_unique.iloc[1]["pident"] < 100
+                ):
+                    emm_typing_results["EMM_type"] += "*"
+                    notes.append(
+                        f"EMM{blast_df_unique.iloc[1]['qseqid'][3:]} with pident {round(blast_df_unique.iloc[1]['pident'],2)} and length {blast_df_unique.iloc[1]['length']}/{blast_df_unique.iloc[1]['qlen']}"
+                    )
 
-            emm_typing_results["ENN_type"] = blast_df_unique.iloc[2]["qseqid"][3:]
-            if (
-                blast_df_unique.iloc[2]["length"] < 180
-                or blast_df_unique.iloc[2]["pident"] < 100
-            ):
-                emm_typing_results["ENN_type"] += "*"
-                notes.append(
-                    f"ENN{blast_df_unique.iloc[2]['qseqid'][3:]} with pident {round(blast_df_unique.iloc[2]['pident'],2)} and length {blast_df_unique.iloc[2]['length']}/{blast_df_unique.iloc[2]['qlen']}"
+                emm_typing_results["ENN_type"] = (
+                    "ENN" + blast_df_unique.iloc[2]["qseqid"][3:]
                 )
-        elif blast_df_unique.shape[0] == 0:
-            notes.append("No blast hits found for EMM genes")
+                if (
+                    blast_df_unique.iloc[2]["length"] < blast_df_unique.iloc[2]["qlen"]
+                    or blast_df_unique.iloc[2]["pident"] < 100
+                ):
+                    emm_typing_results["ENN_type"] += "*"
+                    notes.append(
+                        f"ENN{blast_df_unique.iloc[2]['qseqid'][3:]} with pident {round(blast_df_unique.iloc[2]['pident'],2)} and length {blast_df_unique.iloc[2]['length']}/{blast_df_unique.iloc[2]['qlen']}"
+                    )
+    else:
+        note_to_add = "EMM and EMM-like genes found on multiple contigs"
+        emm_genes = []
+        for index, row in blast_df_unique.iterrows():
+            if row["length"] < row["qlen"] or row["pident"] < 100:
+                emm_genes.append(row["qseqid"][3:] + "*")
+            else:
+                emm_genes.append(row["qseqid"][3:])
+        notes.append(
+            "EMM and EMM-like genes found on multiple contigs. Alleles found: "
+            + "/".join(emm_genes)
+        )
+
     emm_typing_results["emm_typing_notes"] = ", ".join(notes)
     return emm_typing_results
 
@@ -176,7 +215,7 @@ class SpyogenesResults(core.PipelineResults):
     def from_tool_paths(cls, emm_blast_tsv: Path, sample_name=None):
         """
         Alternative constructor for initializing results for single sample,
-        Initializes LegionellaResults instance provided paths to outputs from tools (legionella sbt and lag1 presence blast)
+        Initializes SpyogenesResults instance provided paths to outputs from tools (legionella sbt and lag1 presence blast)
         """
         gas_results = cls.summary(emm_blast_tsv=emm_blast_tsv)
         return cls({sample_name: gas_results})
@@ -185,7 +224,7 @@ class SpyogenesResults(core.PipelineResults):
     def from_tool_paths_dict(cls, file_paths: dict):
         """
         Alternative constructor for initializing results for multiple samples,
-        Initializes LegionellaResults instance by providing a dictionary of paths to outputs from tools (legionella sbt and lag1 presence blast)
+        Initializes SpyogenesResults instance by providing a dictionary of paths to outputs from tools (legionella sbt and lag1 presence blast)
         """
         results_dict = {}
         for sample_name, path_dict in file_paths.items():
@@ -197,7 +236,7 @@ class SpyogenesResults(core.PipelineResults):
     def from_tool_paths_dataframe(cls, file_paths_df: pandas.DataFrame):
         """
         Alternative constructor for initializing results for multiple samples,
-        Initializes LegionellaResults instance by providing a DataFrame of paths to outputs from tools (legionella sbt and lag1 presence blast)
+        Initializes SpyogenesResults instance by providing a DataFrame of paths to outputs from tools (legionella sbt and lag1 presence blast)
         """
         file_paths = file_paths_df.to_dict(orient="index")
         results_dict = {}
@@ -210,7 +249,7 @@ class SpyogenesResults(core.PipelineResults):
     def from_tool_paths_tsv(cls, tool_paths_tsv: Path):
         """
         Alternative constructor for initializing results for multiple samples,
-        Initializes LegionellaResults instance by providing a tsv-file with paths to outputs from tools (legionella sbt and lag1 presence blast)
+        Initializes SpyogenesResults instance by providing a tsv-file with paths to outputs from tools (legionella sbt and lag1 presence blast)
         """
         file_paths_df = pandas.read_csv(tool_paths_tsv, sep="\t")
         file_paths_df.set_index("sample_name", inplace=True, drop=True)
@@ -226,7 +265,7 @@ class SpyogenesResults(core.PipelineResults):
         return results_dict
 
     def __repr__(self):
-        return f"< Legionella analysis results object. {len(self.results_df)} samples with {len(self.results_df.columns)} result variables > "
+        return f"< Spyogenes analysis results object. {len(self.results_df)} samples with {len(self.results_df.columns)} result variables > "
 
 # %% ../nbs/31_Spyogenes_parser.ipynb 9
 @call_parse

ssi_analysis_result_parsers-0.0.9/ssi_analysis_result_parsers/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.0.9"

{ssi_analysis_result_parsers-0.0.7 → ssi_analysis_result_parsers-0.0.9}/ssi_analysis_result_parsers/blast_parser.py

@@ -74,8 +74,8 @@ def extract_presence_absence(
         except pandas.errors.EmptyDataError:
             blast_dict = {}
             print(f"Blast output file {blast_output_tsv} empty. Assuming 0 blast hits.")
-        except Exception as e:
-            print(f"Error parsing blast: e")
+        # except Exception as e:
+        #    print(f"Error parsing blast: e")
         if hits_as_string:
 
             results = []
@@ -105,6 +105,7 @@ def extract_presence_absence(
 
     else:
         print(f"No blast output found at {blast_output_tsv}", file=sys.stderr)
+        return None
 
 
 def extract_allele_matches(
@@ -122,21 +123,38 @@ def extract_allele_matches(
     allele_dict = {}
     detailed_dict = {}
     if os.path.exists(blast_output_tsv):
-        blast_df = pandas.read_csv(blast_output_tsv, sep="\t", header=None)
-        blast_df.columns = tsv_header.split(" ")
-        blast_df.set_index("qseqid", drop=False)
-        blast_df["plen"] = blast_df["length"] / blast_df["qlen"] * 100
-        blast_df[["gene", "allele"]] = blast_df["qseqid"].str.split("_", expand=True)
-        blast_df_unique = (
-            blast_df.sort_values(by=["bitscore"], ascending=False)
-            .groupby("gene")
-            .first()
-        )
-        for gene, d in blast_df_unique.to_dict(orient="index").items():
-            allele_dict[gene] = d["allele"]
-            detailed_dict[gene] = f"{d['allele']}__{d['pident']}__{d['plen']}"
+        try:
+            blast_df = pandas.read_csv(blast_output_tsv, sep="\t", header=None)
+            header_list = tsv_header.split(" ")
+            if len(header_list) == len(blast_df.columns):
+                blast_df.columns = tsv_header.split(" ")
+                blast_df.set_index("qseqid", drop=False)
+                blast_df["plen"] = blast_df["length"] / blast_df["qlen"] * 100
+                blast_df[["gene", "allele"]] = blast_df["qseqid"].str.split(
+                    "_", expand=True
+                )
+                blast_df_unique = (
+                    blast_df.sort_values(by=["bitscore"], ascending=False)
+                    .groupby("gene")
+                    .first()
+                )
+                for gene, d in blast_df_unique.to_dict(orient="index").items():
+                    allele_dict[gene] = d["allele"]
+                    detailed_dict[gene] = f"{d['allele']}__{d['pident']}__{d['plen']}"
+            else:
+                print(
+                    f"Failed to parse {blast_output_tsv}. Number of columns do not match length of provided header string",
+                    file=sys.stderr,
+                )
+                return None
+
+        except pandas.errors.EmptyDataError:
+            detailed_dict = {}
+            allele_dict = {}
+            print(f"Blast output file {blast_output_tsv} empty. Assuming 0 blast hits.")
     else:
         print(f"No blast output found at {blast_output_tsv}", file=sys.stderr)
+        return None
 
     if include_match_stats:
         return detailed_dict

{ssi_analysis_result_parsers-0.0.7 → ssi_analysis_result_parsers-0.0.9/ssi_analysis_result_parsers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ssi_analysis_result_parsers
-Version: 0.0.7
+Version: 0.0.9
 Summary: TODO
 Home-page: https://github.com/thej-ssi/ssi_analysis_result_parsers
 Author: Thor Bech Johannesen

{ssi_analysis_result_parsers-0.0.7 → ssi_analysis_result_parsers-0.0.9}/ssi_analysis_result_parsers.egg-info/SOURCES.txt

@@ -38,6 +38,8 @@ test_input/Spyogenes/emm_typing/test2.mga.blast.tsv
 test_input/Spyogenes/emm_typing/test3.emm.blast.tsv
 test_input/Spyogenes/emm_typing/test4.emm.blast.tsv
 test_input/Spyogenes/emm_typing/test5.emm.blast.tsv
+test_input/Spyogenes/emm_typing/test6.emm.blast.tsv
+test_input/Spyogenes/emm_typing/test7.emm.blast.tsv
 test_input/blast_parser/allele_matches_test.tsv
 test_input/blast_parser/empty_gene_presence_absense_test.tsv
 test_input/blast_parser/gene_presence_absence_test.tsv

ssi_analysis_result_parsers-0.0.9/test_input/Spyogenes/batch_parser_file_paths.tsv

@@ -0,0 +1,10 @@
+sample_name	emm_results
+sample_1	test_input/Spyogenes/emm_typing/test1.emm.blast.tsv
+sample_2	test_input/Spyogenes/emm_typing/test2.emm.blast.tsv
+sample_3	test_input/Spyogenes/emm_typing/test3.emm.blast.tsv
+sample_4	test_input/Spyogenes/emm_typing/test4.emm.blast.tsv
+sample_5	test_input/Spyogenes/emm_typing/test5.emm.blast.tsv
+sample_6	test_input/Spyogenes/emm_typing/test6.emm.blast.tsv
+sample_7	test_input/Spyogenes/emm_typing/test7.emm.blast.tsv
+sample_empty	test_input/empty_file.txt
+sample_nonexist	test_input/files_that_does_not_exist.tsv

ssi_analysis_result_parsers-0.0.9/test_input/Spyogenes/emm_typing/test6.emm.blast.tsv

@@ -0,0 +1,45 @@
+EMM156.0	GAS-2025-0367_2_61.3538	85.556	180	180	1	180	200941	201108	GGATTAGCAAACACAACTGATGTAAAGGCTGAGA--C-T-G--AGCATG---TTGATGTTGTGCTT-T-C-AGCAAAAGAAGCTAACAAAGTATTCGAAGAGCGCAAAGCCTTGGAAAAACAAGCGCGTGATTTGGGTGACACTATTAATCACATGTCACAAACCATTAGTGAGCAAAGC	5.79e-46	178
+EMM156.1	GAS-2025-0367_2_61.3538	85.000	180	180	1	180	200941	201108	GGATTAGCAAACACAACTGATGTAAAGGCTGAGA--C-T-G--AGCA--TG-TTGAT-GT-TG-TGCTTTCAGCAAAAGAAGCTAACAAAGTATTCGAAGAGCGCAAAGCCTTGGAAAAACAAGCGCGTGATTTGGGTGACACTATTAATCACATGTCACAAACCATTAGTGAGCAAAGC	2.69e-44	172
+EMM156.2	GAS-2025-0367_2_61.3538	86.111	180	180	1	180	200941	201108	GGATTAGCAAACACAACTGATGTAAAGGCTGAGA--C-T-G--AGCA--TG-TTGAT-GT-TG-TGCTTTCAGCAAAAGAAGCTAACAAAGTATTCGAAGAGCGCAAAGCCTTGGAAAAACAAGCGCGTGATTTGGGTGACACTATTAATCACATGTCACAAACCATTAGTGAGCAAAGC	1.24e-47	183
+EMM156.3	GAS-2025-0367_2_61.3538	85.556	180	180	1	180	200941	201108	GGATTAGCAAACACAACTGATGTAAAGGCTGAGA--C-T-G--AGCA--TG-TTGAT-GT-TG-TGCTTTCAGCAAAAGAAGCTAACAAAGTATTCGAAGAGCGCAAAGCCTTGGAAAAACAAGCGCGTGATTTGGGTGACACTATTAATCACATGTCACAAACCATTAGTGAGCAAAGC	5.79e-46	178
+EMM156.4	GAS-2025-0367_2_61.3538	85.000	180	180	1	180	200941	201108	GGATTAGCAAACACAACTGATGTAAAGGCTGAGA--C-T-G--AGCA--TG-TTGAT-GT-TG-TGCTTTCAGCAAAAGAAGCTAACAAAGTATTCGAAGAGCGCAAAGCCTTGGAAAAACAAGCGCGTGATTTGGGTGACACTATTAATCACATGTCACAAACCATTAGTGAGCAAAGC	2.69e-44	172
+EMM203.3	GAS-2025-0367_2_61.3538	96.111	180	180	1	180	203502	203681	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	5.51e-81	294
+EMM203.4	GAS-2025-0367_2_61.3538	96.667	180	180	1	180	203502	203681	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	1.18e-82	300
+EMM203.5	GAS-2025-0367_2_61.3538	93.333	180	180	1	180	203502	203681	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	1.20e-72	267
+EMM236.0	GAS-2025-0367_2_61.3538	93.333	180	180	1	180	203502	203681	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	1.20e-72	267
+EMM236.1	GAS-2025-0367_2_61.3538	93.889	180	180	1	180	203502	203681	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	2.58e-74	272
+EMM236.3	GAS-2025-0367_2_61.3538	93.889	180	180	1	180	203502	203681	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	2.58e-74	272
+EMM28.0	GAS-2025-0367_2_61.3538	100.000	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	1.17e-92	333
+EMM28.1	GAS-2025-0367_2_61.3538	98.788	165	180	1	165	202215	202379	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAA	5.51e-81	294
+EMM28.10	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.11	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.12	GAS-2025-0367_2_61.3538	98.333	180	180	1	180	202215	202391	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTA---AAGAAGAAGAACCTAGGTATAAA	1.52e-86	313
+EMM28.13	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.14	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.15	GAS-2025-0367_2_61.3538	98.333	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	1.18e-87	316
+EMM28.16	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.17	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.18	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.19	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.2	GAS-2025-0367_2_61.3538	99.390	164	180	1	164	202215	202378	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGA	4.26e-82	298
+EMM28.20	GAS-2025-0367_2_61.3538	98.889	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	2.53e-89	322
+EMM28.21	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.22	GAS-2025-0367_2_61.3538	98.765	162	180	1	162	202215	202376	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAA	2.56e-79	289
+EMM28.23	GAS-2025-0367_2_61.3538	98.889	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	2.53e-89	322
+EMM28.24	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.25	GAS-2025-0367_2_61.3538	100.000	175	180	1	175	202215	202389	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATA	7.02e-90	324
+EMM28.26	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.27	GAS-2025-0367_2_61.3538	98.889	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	2.53e-89	322
+EMM28.28	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.29	GAS-2025-0367_2_61.3538	98.361	183	180	1	180	202215	202397	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCATTG	3.27e-88	318
+EMM28.3	GAS-2025-0367_2_61.3538	99.394	165	180	1	165	202215	202379	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAA	1.18e-82	300
+EMM28.30	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.31	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.32	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.33	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.4	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.5	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.6	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.7	GAS-2025-0367_2_61.3538	99.383	162	180	1	162	202215	202376	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAA	5.51e-81	294
+EMM28.8	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.9	GAS-2025-0367_2_61.3538	98.333	180	180	1	180	202215	202391	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCT---AAAGAAGAAGAACCTAGGTATAAA	1.52e-86	313

ssi_analysis_result_parsers-0.0.9/test_input/Spyogenes/emm_typing/test7.emm.blast.tsv

@@ -0,0 +1,40 @@
+EMM203.3	GAS-2025-0367_5_42.2241	96.111	180	180	1	180	55602	55781	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	5.51e-81	294
+EMM203.4	GAS-2025-0367_5_42.2241	96.667	180	180	1	180	55602	55781	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	1.18e-82	300
+EMM203.5	GAS-2025-0367_5_42.2241	93.333	180	180	1	180	55602	55781	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	1.20e-72	267
+EMM236.0	GAS-2025-0367_5_42.2241	93.333	180	180	1	180	55602	55781	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	1.20e-72	267
+EMM236.1	GAS-2025-0367_5_42.2241	93.889	180	180	1	180	55602	55781	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	2.58e-74	272
+EMM236.3	GAS-2025-0367_5_42.2241	93.889	180	180	1	180	55602	55781	GGTTTTGCAAACCAAACGGAAGTAAGAGCTGAAGGGGTAAACCCGACTACGAACTTGCCAGAGAAGGCTAAATATGCCGCAGTGAAAGATGAGAATACTGGTTTACGTGGTGATCAGAAAAAATTAGTAAAAAAACTTGAAGAAGAACAAGAGAAGAGCAAAAATCTAGAAAAGCAAAAA	2.58e-74	272
+EMM28.0	GAS-2025-0367_2_61.3538	100.000	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	1.17e-92	333
+EMM28.1	GAS-2025-0367_2_61.3538	98.788	165	180	1	165	202215	202379	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAA	5.51e-81	294
+EMM28.10	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.11	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.12	GAS-2025-0367_2_61.3538	98.333	180	180	1	180	202215	202391	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTA---AAGAAGAAGAACCTAGGTATAAA	1.52e-86	313
+EMM28.13	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.14	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.15	GAS-2025-0367_2_61.3538	98.333	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	1.18e-87	316
+EMM28.16	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.17	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.18	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.19	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.2	GAS-2025-0367_2_61.3538	99.390	164	180	1	164	202215	202378	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGA	4.26e-82	298
+EMM28.20	GAS-2025-0367_2_61.3538	98.889	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	2.53e-89	322
+EMM28.21	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.22	GAS-2025-0367_2_61.3538	98.765	162	180	1	162	202215	202376	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAA	2.56e-79	289
+EMM28.23	GAS-2025-0367_2_61.3538	98.889	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	2.53e-89	322
+EMM28.24	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.25	GAS-2025-0367_2_61.3538	100.000	175	180	1	175	202215	202389	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATA	7.02e-90	324
+EMM28.26	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.27	GAS-2025-0367_2_61.3538	98.889	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	2.53e-89	322
+EMM28.28	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.29	GAS-2025-0367_2_61.3538	98.361	183	180	1	180	202215	202397	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCATTG	3.27e-88	318
+EMM28.3	GAS-2025-0367_2_61.3538	99.394	165	180	1	165	202215	202379	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAA	1.18e-82	300
+EMM28.30	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.31	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.32	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.33	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.4	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.5	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.6	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.7	GAS-2025-0367_2_61.3538	99.383	162	180	1	162	202215	202376	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAA	5.51e-81	294
+EMM28.8	GAS-2025-0367_2_61.3538	99.444	180	180	1	180	202215	202394	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCTAAAGAAGAAGAACCTAGGTATAAAGCA	5.43e-91	327
+EMM28.9	GAS-2025-0367_2_61.3538	98.333	180	180	1	180	202215	202391	GGCTTTGCAAACCAAACAGAAGTTAAGGCTGCGGAGTCTCCAAAAAGTACTGAGACTTCTGCTAATGGAGCTGATAAATTAGCTGATGCATACAACACATTGCTTACTGAACATGAGAAACTCAGAGATGAGTATTATACATTAATTGATGCT---AAAGAAGAAGAACCTAGGTATAAA	1.52e-86	313

ssi_analysis_result_parsers-0.0.7/ssi_analysis_result_parsers/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.0.7"

ssi_analysis_result_parsers-0.0.7/test_input/Spyogenes/batch_parser_file_paths.tsv

@@ -1,5 +0,0 @@
-sample_name	emm_results
-sample_1	test_input/Spyogenes/emm_typing/test1.emm.blast.tsv
-sample_2	test_input/Spyogenes/emm_typing/test2.emm.blast.tsv
-sample_3	test_input/files_that_does_not_exist.tsv
-sample_4	test_input/empty_file.txt