ssi-analysis-result-parsers 0.0.14__py3-none-any.whl → 0.0.15__py3-none-any.whl

ssi_analysis_result_parsers/Ecoli_parser.py

@@ -5,8 +5,7 @@ __all__ = ['thresholds', 'samplesheet_path', 'output_dir', 'output_path', 'sampl
            'output_cols', 'output_initial_cols', 'output_specific_cols', 'ERR3528110_res_path', 'ERR3528110_input_df',
            'ERR3528110_row', 'gene_hits', 'parsed_hits', 'O_gene_alleles', 'H_gene_alleles', 'O_type', 'H_type',
            'O_gene_keys', 'H_gene_keys', 'O_genes_no', 'H_genes_no', 'ERR14229029_row', 'ERR14229029_expected_values',
-           'ERR14229029_values', 'test_cases', 'setup_logging', 'get_threshold', 'process_res_file', 'EcoliResults',
-           'ecoli_parser']
+           'ERR14229029_values', 'setup_logging', 'get_threshold', 'process_res_file', 'EcoliResults', 'ecoli_parser']
 
 # %% ../nbs/49_Ecoli_parser.ipynb 3
 import os
@@ -501,169 +500,3 @@ for col, actual, expected in zip(
         assert pd.isna(actual), f"{col}: Expected NaN, got {actual}"
     else:
         assert actual == expected, f"{col}: Expected '{expected}', got '{actual}'"
-
-# %% ../nbs/49_Ecoli_parser.ipynb 19
-import os
-from tempfile import TemporaryDirectory
-from pathlib import Path
-
-test_cases = [
-    # sample_name, res_content, expected_oh, expected_stx, expected_eae, expected_ehxA
-    (
-        "sample1",
-        "1__wzx__O103__X\t100\t100\t60\n2__wzy__O103__X\t100\t100\t65\n3__fliC__H2__X\t100\t100\t70",
-        "O103;H2",
-        "-",
-        "-",
-        "-",
-    ),
-    (
-        "sample2",
-        "1__wzt__O8__X\t100\t100\t60\n2__wzm__O8__X\t100\t100\t65\n3__fliC__H10__X\t100\t100\t70\n4__stx2__stx2-a__X\t100\t100\t90\n5__eae__eae-5__X\t100\t100\t80",
-        "O8;H10",
-        "stx2-a",
-        "Positive",
-        "-",
-    ),
-    ("sample3", "1__fliC__H7__X\t100\t100\t70", "-;H7", "-", "-", "-"),
-    (
-        "sample4",
-        "bad_line\n2__wzy__O111__X\t100\t100\t70\n3__fliC__H11__X\t100\t100\t70",
-        "-;H11",
-        "-",
-        "-",
-        "-",
-    ),
-    ("sample5", "", "-;-", "-", "-", "-"),
-    (
-        "sample6",
-        "1__wzx__O157__X\t100\t100\t60\n2__wzy__O157__X\t100\t100\t65\n3__wzt__O8__X\t100\t100\t60\n4__wzm__O8__X\t100\t100\t65\n5__fli__H2__X\t100\t100\t70",
-        "-;H2",
-        "-",
-        "-",
-        "-",
-    ),
-    (
-        "sample7",
-        "1__wzx__O157__X\t100\t100\t60\n2__wzy__O111__X\t100\t100\t65\n3__fliC__H9__X\t100\t100\t70",
-        "-;H9",
-        "-",
-        "-",
-        "-",
-    ),
-    (
-        "sample8",
-        "1__fli__H1__X\t100\t100\t70\n2__fliC__H12__X\t100\t100\t70",
-        "-;H1",
-        "-",
-        "-",
-        "-",
-    ),
-    (
-        "sample9",
-        "1__wzx__O157__X\t100\t100\t60\n2__wzy__O157__X\t100\t100\t65\n3__wzt__O8__X\t100\t100\t60\n4__wzm__O8__X\t100\t100\t65\n5__fliC__H10__X\t100\t100\t70\n6__fli__H2__X\t100\t100\t70\n7__stx1__stx1-a__X\t100\t100\t90\n8__stx2__stx2-d__X\t100\t100\t90\n9__stx2__stx2-a__X\t100\t100\t90\n10__eae__eae-42-5__X\t100\t100\t80\n11__ehxA__ehxA-7__X\t100\t100\t80",
-        "-;H2",
-        "stx1-a;stx2-a;stx2-d",
-        "Positive",
-        "Positive",
-    ),
-    (
-        "sample10",
-        "1__adk__adk__X\t100\t100\t70\n2__fliC__H4__X\t100\t100\t70",
-        "-;H4",
-        "-",
-        "-",
-        "-",
-    ),
-    (
-        "sample11",
-        "1__eae__eae-1__X\t100\t94\t70\n2__fliC__H6__X\t100\t100\t70",
-        "-;H6",
-        "-",
-        "-",
-        "-",
-    ),
-    (
-        "sample12",
-        "1__stx1__stx1a__X\t100\t100\t80\n2__stx2__stx2c__X\t100\t100\t85\n3__fli__H21__X\t100\t100\t70",
-        "-;H21",
-        "stx1a;stx2c",
-        "-",
-        "-",
-    ),
-]
-
-for (
-    sample_name,
-    res_content,
-    expected_oh,
-    expected_stx,
-    expected_eae,
-    expected_ehxA,
-) in test_cases:
-    with TemporaryDirectory() as tmpdir:
-        tmpdir = Path(tmpdir)
-        os.chdir(tmpdir)
-
-        res_dir = tmpdir / f"examples/Results/{sample_name}/kma"
-        res_dir.mkdir(parents=True)
-        res_file = res_dir / f"{sample_name}.res"
-        res_file.write_text(
-            "#Template\tTemplate_Coverage\tQuery_Identity\tDepth\n" + res_content
-        )
-
-        sheet = tmpdir / "samplesheet.tsv"
-        sheet.write_text(
-            "sample_name\tIllumina_read_files\tNanopore_read_file\tassembly_file\torganism\tvariant\tnotes\n"
-            f"{sample_name}\tread1.fastq,read2.fastq\t-\t-\tEcoli\t-\t-\n"
-        )
-
-        results = EcoliResults.from_samplesheet(sheet)
-        df = results.results_df
-        row = df.iloc[0]
-
-        # general output and functionality test
-        assert row["sample_name"] == sample_name
-
-        if row["OH"] != expected_oh:
-            raise AssertionError(
-                f"\nSample: {sample_name}\nExpected OH: {expected_oh}\nActual OH: {row['OH']}"
-            )
-        assert row["OH"] == expected_oh
-
-        if row["stx"] != expected_stx:
-            raise AssertionError(
-                f"\nSample: {sample_name}\nExpected stx: {expected_stx}\nActual stx: {row['stx']}"
-            )
-        assert row["stx"] == expected_stx
-
-        if row["eae"] != expected_eae:
-            raise AssertionError(
-                f"\nSample: {sample_name}\nExpected eae: {expected_eae}\nActual eae: {row['eae']}"
-            )
-        assert row["eae"] == expected_eae
-
-        if row["ehxA"] != expected_ehxA:
-            raise AssertionError(
-                f"\nSample: {sample_name}\nExpected ehxA: {expected_ehxA}\nActual ehxA: {row['ehxA']}"
-            )
-        assert row["ehxA"] == expected_ehxA
-
-        # sample specific information tests
-
-        # without confliciting O and H typing, the OH column should be filled and the remaining four genes empty
-        if sample_name == "sample1":
-            assert row["wzx"] == "-"
-            assert row["wzy"] == "-"
-            assert row["wzt"] == "-"
-            assert row["wzm"] == "-"
-        # with conflicts the OH should remain empty and the four 'conflicting' gene information remain filled
-        elif sample_name == "sample6":
-            assert row["wzx"] == "O157"
-            assert row["wzy"] == "O157"
-            assert row["wzt"] == "O8"
-            assert row["wzm"] == "O8"
-        elif sample_name == "sample10":
-            assert row["Other"] == "adk"
-
-print("All 12 syntehtic E. coli sample inline tests passed.")

ssi_analysis_result_parsers/Hinfluenzae_parser.py

@@ -0,0 +1,302 @@
+# AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/38_Hinfluenzae_parser.ipynb.
+
+# %% auto 0
+__all__ = ['get_biotype_from_gene_presence', 'extract_hicap_results', 'extract_ariba_ftsI_snps', 'HinfluenzaeResults',
+           'Hinfluenzae_parser', 'Hinfluenzae_batch_parser']
+
+# %% ../nbs/38_Hinfluenzae_parser.ipynb 3
+# standard libs
+import os
+import re
+
+# Common to template
+# add into settings.ini, requirements, package name is python-dotenv, for conda build ensure `conda config --add channels conda-forge`
+import dotenv  # for loading config from .env files, https://pypi.org/project/python-dotenv/
+import envyaml  # Allows to loads env vars into a yaml file, https://github.com/thesimj/envyaml
+import fastcore  # To add functionality related to nbdev development, https://github.com/fastai/fastcore/
+from fastcore import (
+    test,
+)
+from fastcore.script import (
+    call_parse,
+)  # for @call_parse, https://fastcore.fast.ai/script
+import json  # for nicely printing json and yaml
+
+# import functions from core module (optional, but most likely needed).
+from ssi_analysis_result_parsers import (
+    core,
+    blast_parser,
+)
+
+# from ssi_analysis_result_parsers.blast_parser import extract_presence_absence
+
+# Project specific libraries
+from pathlib import Path
+import pandas
+import numpy
+import sys
+
+# %% ../nbs/38_Hinfluenzae_parser.ipynb 6
+def get_biotype_from_gene_presence(biotype_gene_presence_dict: Path) -> dict:
+    """
+    Convert biotype gene presence dict to biotype
+    """
+    if biotype_gene_presence_dict:
+        if not biotype_gene_presence_dict["indole"] == "0":
+            if not biotype_gene_presence_dict["urease"] == "0":
+                if not biotype_gene_presence_dict["ODC"] == "0":
+                    biotype = "I"
+                else:
+                    biotype = "II"
+            else:
+                if not biotype_gene_presence_dict["ODC"] == "0":
+                    biotype = "V"
+                else:
+                    biotype = "VII"
+        else:
+            if not biotype_gene_presence_dict["urease"] == "0":
+                if not biotype_gene_presence_dict["ODC"] == "0":
+                    biotype = "IV"
+                else:
+                    biotype = "III"
+            else:
+                if not biotype_gene_presence_dict["ODC"] == "0":
+                    biotype = "VI"
+                else:
+                    biotype = "VIII"
+        return {"biotype": biotype}
+    else:
+        print(
+            f"Nonetype input provided for biotype gene presence. Cannot determine biotype."
+        )
+        return None
+
+
+def extract_hicap_results(hicap_tsv: Path):
+    if hicap_tsv.exists():
+        try:
+            df = pandas.read_csv(hicap_tsv, sep="\t")
+            if df.shape[0] > 0:
+                serotype = df.iloc[0]["predicted_serotype"]
+                serotype_attributes = df.iloc[0]["attributes"]
+                serotype_genes = df.iloc[0]["genes_identified"]
+            else:
+                print(f"Hicap output file empty at {hicap_tsv}", file=sys.stderr)
+                return None
+        except pandas.errors.EmptyDataError:
+            print(f"Hicap output file empty at {hicap_tsv}", file=sys.stderr)
+            return None
+    else:
+        serotype = "-"
+        serotype_attributes = "no_capsule_genes_found"
+        serotype_genes = "-"
+
+    return {
+        "serotype": serotype,
+        "serotype_attributes": serotype_attributes,
+        "serotype_genes": serotype_genes,
+    }
+
+
+def extract_ariba_ftsI_snps(ariba_output_tsv: Path, ftsI_types_tsv: Path):
+    if not ftsI_types_tsv.exists():
+        print(f"Failed to load ftsI types table at {ftsI_types_tsv}")
+        return None
+    elif ariba_output_tsv.exists():
+        ftsI_types = {}
+        ftsI_table_snps = []
+        with open(ftsI_types_tsv) as f:
+            for line in f:
+                line = line.rstrip("\n").split("\t")
+                if line[0] == "pos":
+                    positions = line[1:]
+                elif line[0] == "Ref":
+                    refs = line[1:]
+                elif line[0] == "Diverse":
+                    snps = line[1:]
+                    for n in range(len(snps)):
+                        snp_split = snps[n].split("/")
+                        for snp in snp_split:
+                            ftsI_table_snps.append(refs[n] + positions[n] + snp)
+                else:
+                    type = line[0]
+                    vars = line[1:]
+                    type_vars = []
+                    for n in range(len(vars)):
+                        var = vars[n]
+                        if var != "" and var != " ":
+                            type_vars.append(refs[n] + positions[n] + var)
+                    ftsI_types[type] = type_vars
+
+        change_list = []
+        ftsI_gene_snps = []
+        with open(ariba_output_tsv) as f:
+            for line in f:
+                line = line.rstrip("\n").split("\t")
+                if line[0] != "#ariba_ref_name":
+                    change = line[18]
+                    ftsI_gene_snps.append(change)
+                    if change in ftsI_table_snps:
+                        change_list.append(change)
+
+        match_var_counts = {}
+        for type in ftsI_types:
+            var_list = ftsI_types[type]
+            match_var_count = 0
+            for var in var_list:
+                if var in change_list:
+                    match_var_count += 1
+            match_var_counts[type] = [match_var_count, len(var_list)]
+        best_match = 0
+        best_type = "-"
+        for type in match_var_counts:
+            check_list = match_var_counts[type]
+            if check_list[0] == check_list[1] and check_list[0] > best_match:
+                best_match = check_list[0]
+                best_type = type
+    else:
+        print(f"No ariba report found at {ariba_output_tsv}")
+        return None
+    return {
+        "ftsI_type": best_type,
+        "key_ftsI_snps": ",".join(change_list),
+        "all_ftsI_snps": ",".join(ftsI_gene_snps),
+    }
+
+
+class HinfluenzaeResults(core.PipelineResults):
+
+    @classmethod
+    def from_tool_paths(
+        cls,
+        ftsI_ariba_tsv: Path,
+        hicap_tsv: Path,
+        biotype_blast_tsv: Path,
+        ftsI_types_tsv: Path,
+        sample_name=None,
+    ):
+        """
+        Alternative constructor for initializing results for single sample,
+        Initializes HinfluenzaeResults instance provided paths to outputs from tools (legionella sbt and lag1 presence blast)
+        """
+        hinfluenze_results = cls.summary(
+            ftsI_ariba_tsv=ftsI_ariba_tsv,
+            hicap_tsv=hicap_tsv,
+            biotype_blast_tsv=biotype_blast_tsv,
+            ftsI_types_tsv=ftsI_types_tsv,
+        )
+        return cls({sample_name: hinfluenze_results})
+
+    @classmethod
+    def from_tool_paths_dict(cls, file_paths: dict):
+        """
+        Alternative constructor for initializing results for multiple samples,
+        Initializes HinfluenzaeResults 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():
+            hinfluenze_results = cls.summary(
+                ftsI_ariba_tsv=Path(path_dict["ftsI_ariba_results"]),
+                hicap_tsv=Path(path_dict["hicap_results"]),
+                biotype_blast_tsv=Path(path_dict["biotype_results"]),
+                ftsI_types_tsv=Path(path_dict["ftsI_types_tsv"]),
+            )
+            results_dict[sample_name] = hinfluenze_results
+        return cls(results_dict)
+
+    @classmethod
+    def from_tool_paths_dataframe(cls, file_paths_df: pandas.DataFrame):
+        """
+        Alternative constructor for initializing results for multiple samples,
+        Initializes HinfluenzaeResults instance by providing a DataFrame of paths to outputs from tools (legionella sbt and lag1 presence blast)
+        """
+        file_paths_df.replace(numpy.nan, None, inplace=True)
+        file_paths = file_paths_df.to_dict(orient="index")
+        results_dict = {}
+        for sample_name, path_dict in file_paths.items():
+            hinfluenzae_results = cls.summary(
+                ftsI_ariba_tsv=Path(path_dict["ftsI_ariba_results"]),
+                hicap_tsv=Path(path_dict["hicap_results"]),
+                biotype_blast_tsv=Path(path_dict["biotype_results"]),
+                ftsI_types_tsv=Path(path_dict["ftsI_types_tsv"]),
+            )
+            results_dict[sample_name] = hinfluenzae_results
+        return cls(results_dict)
+
+    @classmethod
+    def from_tool_paths_tsv(cls, tool_paths_tsv: Path):
+        """
+        Alternative constructor for initializing results for multiple samples,
+        Initializes HinfluenzaeResults 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)
+        return cls.from_tool_paths_dataframe(file_paths_df)
+
+    @staticmethod
+    def summary(
+        ftsI_ariba_tsv: Path,
+        hicap_tsv: Path,
+        biotype_blast_tsv: Path,
+        ftsI_types_tsv: Path,
+    ) -> dict:
+        ftsI_results = extract_ariba_ftsI_snps(
+            ariba_output_tsv=ftsI_ariba_tsv, ftsI_types_tsv=ftsI_types_tsv
+        )
+        hicap_results = extract_hicap_results(hicap_tsv=hicap_tsv)
+        biotype_gene_dict = blast_parser.extract_presence_absence(
+            blast_output_tsv=biotype_blast_tsv,
+            hits_as_string=False,
+            include_match_stats=True,
+            gene_names=["indole", "urease", "ODC"],
+        )
+        biotype_results = get_biotype_from_gene_presence(
+            biotype_gene_presence_dict=biotype_gene_dict
+        )
+        results_dict = core.update_results_dict(
+            ftsI_results, hicap_results, new_duplicate_key_prefix="hicap:"
+        )
+        results_dict = core.update_results_dict(
+            results_dict, biotype_results, old_duplicate_key_prefix="_"
+        )
+        results_dict = core.update_results_dict(
+            results_dict, biotype_gene_dict, old_duplicate_key_prefix="biotype:"
+        )
+        if results_dict is None:
+            return {}
+        return results_dict
+
+    def __repr__(self):
+        return f"< Hinfluenzae analysis results object. {len(self.results_df)} samples with {len(self.results_df.columns)} result variables >"
+
+# %% ../nbs/38_Hinfluenzae_parser.ipynb 9
+@call_parse
+def Hinfluenzae_parser(
+    ftsI_ariba_tsv: Path = None,  # Path to report.tsv from ftsI ariba output
+    hicap_tsv: Path = None,  #  Path to hicap tsv output
+    biotype_blast_tsv: Path = None,  #  Path to output from biotype gene blast. Generated with blastn -query biotype_genes.fasta -subject assembly.fasta -outfmt "6 qseqid sseqid pident length qlen qstart qend sstart send sseq evalue bitscore"
+    ftsI_types_tsv: Path = None,  #  Path to table to convert ftsI snps to ftsI types
+    output_file: Path = None,  # Path to output tsv
+    sample_name: str = None,
+) -> None:
+    """ """
+    hinfluenze_results = HinfluenzaeResults.from_tool_paths(
+        ftsI_ariba_tsv=ftsI_ariba_tsv,
+        hicap_tsv=hicap_tsv,
+        biotype_blast_tsv=biotype_blast_tsv,
+        ftsI_types_tsv=ftsI_types_tsv,
+        sample_name=sample_name,
+    )
+    hinfluenze_results.write_tsv(output_file=output_file)
+
+
+@call_parse
+def Hinfluenzae_batch_parser(
+    file_path_tsv: Path = None,  # Path to tsv containing file paths to the outputs from tools to be parsed. Must contain headers "sample_name", "sbt_results", and "lag1_blast_results"
+    output_file: Path = None,  # Path to output tsv
+) -> None:
+    """ """
+    hinfluenze_results = HinfluenzaeResults.from_tool_paths_tsv(
+        tool_paths_tsv=file_path_tsv
+    )
+    hinfluenze_results.write_tsv(output_file)

ssi_analysis_result_parsers/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.13"
+__version__ = "0.0.15"

ssi_analysis_result_parsers/_modidx.py

@@ -25,6 +25,30 @@ d = { 'settings': { 'branch': 'main',
                                                                                                                          'ssi_analysis_result_parsers/Ecoli_parser.py'),
                                                           'ssi_analysis_result_parsers.Ecoli_parser.setup_logging': ( 'ecoli_parser.html#setup_logging',
                                                                                                                       'ssi_analysis_result_parsers/Ecoli_parser.py')},
+            'ssi_analysis_result_parsers.Hinfluenzae_parser': { 'ssi_analysis_result_parsers.Hinfluenzae_parser.HinfluenzaeResults': ( 'hinfluenzae_parser.html#hinfluenzaeresults',
+                                                                                                                                       'ssi_analysis_result_parsers/Hinfluenzae_parser.py'),
+                                                                'ssi_analysis_result_parsers.Hinfluenzae_parser.HinfluenzaeResults.__repr__': ( 'hinfluenzae_parser.html#hinfluenzaeresults.__repr__',
+                                                                                                                                                'ssi_analysis_result_parsers/Hinfluenzae_parser.py'),
+                                                                'ssi_analysis_result_parsers.Hinfluenzae_parser.HinfluenzaeResults.from_tool_paths': ( 'hinfluenzae_parser.html#hinfluenzaeresults.from_tool_paths',
+                                                                                                                                                       'ssi_analysis_result_parsers/Hinfluenzae_parser.py'),
+                                                                'ssi_analysis_result_parsers.Hinfluenzae_parser.HinfluenzaeResults.from_tool_paths_dataframe': ( 'hinfluenzae_parser.html#hinfluenzaeresults.from_tool_paths_dataframe',
+                                                                                                                                                                 'ssi_analysis_result_parsers/Hinfluenzae_parser.py'),
+                                                                'ssi_analysis_result_parsers.Hinfluenzae_parser.HinfluenzaeResults.from_tool_paths_dict': ( 'hinfluenzae_parser.html#hinfluenzaeresults.from_tool_paths_dict',
+                                                                                                                                                            'ssi_analysis_result_parsers/Hinfluenzae_parser.py'),
+                                                                'ssi_analysis_result_parsers.Hinfluenzae_parser.HinfluenzaeResults.from_tool_paths_tsv': ( 'hinfluenzae_parser.html#hinfluenzaeresults.from_tool_paths_tsv',
+                                                                                                                                                           'ssi_analysis_result_parsers/Hinfluenzae_parser.py'),
+                                                                'ssi_analysis_result_parsers.Hinfluenzae_parser.HinfluenzaeResults.summary': ( 'hinfluenzae_parser.html#hinfluenzaeresults.summary',
+                                                                                                                                               'ssi_analysis_result_parsers/Hinfluenzae_parser.py'),
+                                                                'ssi_analysis_result_parsers.Hinfluenzae_parser.Hinfluenzae_batch_parser': ( 'hinfluenzae_parser.html#hinfluenzae_batch_parser',
+                                                                                                                                             'ssi_analysis_result_parsers/Hinfluenzae_parser.py'),
+                                                                'ssi_analysis_result_parsers.Hinfluenzae_parser.Hinfluenzae_parser': ( 'hinfluenzae_parser.html#hinfluenzae_parser',
+                                                                                                                                       'ssi_analysis_result_parsers/Hinfluenzae_parser.py'),
+                                                                'ssi_analysis_result_parsers.Hinfluenzae_parser.extract_ariba_ftsI_snps': ( 'hinfluenzae_parser.html#extract_ariba_ftsi_snps',
+                                                                                                                                            'ssi_analysis_result_parsers/Hinfluenzae_parser.py'),
+                                                                'ssi_analysis_result_parsers.Hinfluenzae_parser.extract_hicap_results': ( 'hinfluenzae_parser.html#extract_hicap_results',
+                                                                                                                                          'ssi_analysis_result_parsers/Hinfluenzae_parser.py'),
+                                                                'ssi_analysis_result_parsers.Hinfluenzae_parser.get_biotype_from_gene_presence': ( 'hinfluenzae_parser.html#get_biotype_from_gene_presence',
+                                                                                                                                                   'ssi_analysis_result_parsers/Hinfluenzae_parser.py')},
             'ssi_analysis_result_parsers.Legionella_parser': { 'ssi_analysis_result_parsers.Legionella_parser.LegionellaResults': ( 'legionella_parser.html#legionellaresults',
                                                                                                                                     'ssi_analysis_result_parsers/Legionella_parser.py'),
                                                                'ssi_analysis_result_parsers.Legionella_parser.LegionellaResults.__repr__': ( 'legionella_parser.html#legionellaresults.__repr__',

{ssi_analysis_result_parsers-0.0.14.dist-info → ssi_analysis_result_parsers-0.0.15.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ssi_analysis_result_parsers
-Version: 0.0.14
+Version: 0.0.15
 Summary: TODO
 Home-page: https://github.com/thej-ssi/ssi_analysis_result_parsers
 Author: Thor Bech Johannesen

{ssi_analysis_result_parsers-0.0.14.dist-info → ssi_analysis_result_parsers-0.0.15.dist-info}/RECORD

@@ -1,21 +1,29 @@
-ssi_analysis_result_parsers/Ecoli_parser.py,sha256=lKNnx27KqxpX3yv1RAP-sBATMGf9yjfSs4-d50mR2cA,22704
+ssi_analysis_result_parsers/Ecoli_parser.py,sha256=IQDbTPxvaQBf3el92_76QQ3prA2HG930yFgqYibFmEQ,17437
+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/__init__.py,sha256=SxvRes_80c-42zwvn5BXPvpGVs_EZ69FUEtUBF1k9Ts,23
-ssi_analysis_result_parsers/_modidx.py,sha256=rrpJq1GcgPx34ag7bGe6VvBl4v-tC-ErTTvYAjHW7uI,22865
+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
 ssi_analysis_result_parsers/core.py,sha256=8CzFMDrGJ24D9aoIebLsG8tx-OxvYJod1cxBITqNfaY,12258
 ssi_analysis_result_parsers/hello_world.py,sha256=jpN94sqYuNHqUbUZMCJ35qGY5iLPB_emucgnDGDUk_U,1895
 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-0.0.14.dist-info/licenses/LICENSE,sha256=p6aTb6QIfqyZ2Uux2VjV4F2zthdUSHZOjB4mfwGc7fo,1094
+ssi_analysis_result_parsers-0.0.15.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
 test_input/Ecoli/ERR3528110.res,sha256=DmiDRfX9LPypAEzVeO1RHaPoqEpZwq8ZtQDJ1KOWwHc,461
 test_input/Ecoli/samplesheet.tsv,sha256=sSPrVrloOWvfmnp2Lnn8H6mCkiWsZUFV0wrovk3jH-Q,416
+test_input/Hinfluenzae/.DS_Store,sha256=esAD8NJsWOrKyrRnaO45PG4-nf0yXOlSxp2Is19cRVA,6148
+test_input/Hinfluenzae/batch_parser_file_paths.tsv,sha256=K8KLz08wNpK4buW_Q1ifsyFJpua5C-I8YdQ2XUCVKgc,540
+test_input/Hinfluenzae/ariba_ftsI/ftsI_types_table.txt,sha256=X8GSHK6snQ2O-4hlYRaPg_aw7wunQqhIy2IqYhTzmPA,725
+test_input/Hinfluenzae/ariba_ftsI/sample1.ftsI.ariba.tsv,sha256=9aOfC082Vcim7-2xUvJ6fE9X3098oOnu-O0_okimiqQ,955
+test_input/Hinfluenzae/ariba_ftsI/sample2.ftsI.ariba.tsv,sha256=Q_vOwfMzGoK5Cj6yTXz8WRGR8rlD_XQtBcksUu1PTf4,786
+test_input/Hinfluenzae/biotype/sample1.biotype.blast.tsv,sha256=i6fmGIVzOX-LU6Eev2sr4u8921ULZPOyTLEdRoTORU4,4036
+test_input/Hinfluenzae/hicap/sample1.hicap.tsv,sha256=wU935eMzMSkg6s9-9c6XJZfe-VfzkLtelMV31T8zVRI,346
 test_input/Legionella/batch_parser_file_paths.tsv,sha256=AikBS_Ez1xO3UrEQ19AY3z6drBDdMAiSGK66NLeyYj4,356
 test_input/Legionella/lag-1_blast.tsv,sha256=MN5QL_iBn9gQ8VTYEcTnT0JwKgpkD8G15-QFOrSWxkU,1133
 test_input/Legionella/lag-1_blast_2.tsv,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -46,8 +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-0.0.14.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,,
+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-0.0.14.dist-info → ssi_analysis_result_parsers-0.0.15.dist-info}/entry_points.txt

@@ -1,6 +1,8 @@
 [console_scripts]
 blast_parser_allele_matches = ssi_analysis_result_parsers.blast_parser:allele_matches
 blast_parser_presence_absence = ssi_analysis_result_parsers.blast_parser:presence_absence
+get_Hinfluenzae_results = ssi_analysis_result_parsers.Hinfluenzae_parser:Hinfluenzae_parser
+get_Hinfluenzae_results_batch = ssi_analysis_result_parsers.Hinfluenzae_parser:Hinfluenzae_batch_parser
 get_Nmeningitidis_results = ssi_analysis_result_parsers.Nmeningitidis_parser:Nmeningitidis_parser
 get_Nmeningitidis_results_batch = ssi_analysis_result_parsers.Nmeningitidis_parser:Nmeningitidis_batch_parser
 get_Spyogenes_results = ssi_analysis_result_parsers.Spyogenes_parser:Spyogenes_parser

test_input/Hinfluenzae/ariba_ftsI/ftsI_types_table.txt

@@ -0,0 +1,12 @@
+pos	311	337	350	352	357	368	377	385	389	437	443	449	490	501	502	511	517	526	528	530	532	547	562	569	586
+Ref	S	A	D	S	S	A	M	S	L	A	T	I	G	R	A	V	R	N	Y	A	T	V	V	N	A
+I	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	H	 	 	 	 	 	 	 	 
+IIa	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	K	 	 	 	 	 	 	 
+IIb	 	 	 	 	 	 	 	 	 	 	 	 	 	 	V	 	 	K	 	 	 	 	 	 	 
+IIc	 	 	 	 	 	 	 	 	 	 	 	 	 	 	T	 	 	K	 	 	 	 	 	 	 
+IId	 	 	 	 	 	 	 	 	 	 	 	V	 	 	 	 	 	K	 	 	 	 	 	 	 
+III	 	 	 	 	 	 	 	T	 	 	 	 	 	 	 	 	 	K	 	 	 	 	 	 	 
+III+	 	 	 	 	 	 	 	T	F	 	 	 	 	 	 	 	 	K	 	 	 	 	 	 	 
+III like	 	 	 	 	 	 	 	T	 	 	 	 	 	 	 	 	H	 	 	 	 	 	 	 	 
+III like +	 	 	 	 	 	 	 	T	F	 	 	 	 	 	 	 	H	 	 	 	 	 	 	 	 
+Diverse	P	V/N	N	T/N/F	N	T	I	T	F	S	A	V	E	E/L/H	T/V	A	H	K	H	S	S	I	L	S	S

test_input/Hinfluenzae/ariba_ftsI/sample1.ftsI.ariba.tsv

@@ -0,0 +1,5 @@
+#ariba_ref_name	ref_name	gene	var_only	flag	reads	cluster	ref_len	ref_base_assembled	pc_ident	ctg	ctg_len	ctg_cov	known_var	var_type	var_seq_type	known_var_change	has_known_var	ref_ctg_change	ref_ctg_effect	ref_start	ref_end	ref_nt	ctg_start	ctg_end	ctg_nt	smtls_total_depth	smtls_nts	smtls_nts_depth	var_description	free_text
+ftsI	ftsI	1	0	539	1394	cluster	1833	1833	99.51	cluster.l15.c4.ctg.1	2675	74.5	0	.	p	.	0	A22T	NONSYN	64	66	GCA	560	562	ACA	69;69;72	A;C;A,C	58;57;59,1	.	.
+ftsI	ftsI	1	0	539	1394	cluster	1833	1833	99.51	cluster.l15.c4.ctg.1	2675	74.5	0	.	p	.	0	A239E	NONSYN	715	717	GCA	1211	1213	GAA	124;124;129	G;A;A	99;99;103	.	.
+ftsI	ftsI	1	0	539	1394	cluster	1833	1833	99.51	cluster.l15.c4.ctg.1	2675	74.5	0	.	p	.	0	I475L	NONSYN	1423	1425	ATT	1919	1921	CTT	100;98;98	C;T;T	88;86;85	.	.
+ftsI	ftsI	1	0	539	1394	cluster	1833	1833	99.51	cluster.l15.c4.ctg.1	2675	74.5	0	.	p	.	0	E603D	NONSYN	1807	1809	GAA	2303	2305	GAT	84;84;84	G;A;T	68;68;68	.	.

test_input/Hinfluenzae/ariba_ftsI/sample2.ftsI.ariba.tsv

@@ -0,0 +1,4 @@
+#ariba_ref_name	ref_name	gene	var_only	flag	reads	cluster	ref_len	ref_base_assembled	pc_ident	ctg	ctg_len	ctg_cov	known_var	var_type	var_seq_type	known_var_change	has_known_var	ref_ctg_change	ref_ctg_effect	ref_start	ref_end	ref_nt	ctg_start	ctg_end	ctg_nt	smtls_total_depth	smtls_nts	smtls_nts_depth	var_description	free_text
+ftsI	ftsI	1	0	539	758	cluster	1833	1833	99.56	cluster.l15.c4.ctg.1	2736	40.8	0	.	p	.	0	P31S	NONSYN	91	93	CCT	576	578	TCT	38;39;39	T;C;T	35;38;36	.	.
+ftsI	ftsI	1	0	539	758	cluster	1833	1833	99.56	cluster.l15.c4.ctg.1	2736	40.8	0	.	p	.	0	K310E	NONSYN	928	930	AAA	1413	1415	GAA	62;62;62	G;A;A	58;58;58	.	.
+ftsI	ftsI	1	0	539	758	cluster	1833	1833	99.56	cluster.l15.c4.ctg.1	2736	40.8	0	.	p	.	0	V547I	NONSYN	1639	1641	GTT	2124	2126	ATT	51;51;51	A;T;T	46;45;45	.	.

test_input/Hinfluenzae/batch_parser_file_paths.tsv

@@ -0,0 +1,5 @@
+sample_name	biotype_results	ftsI_ariba_results	hicap_results	ftsI_types_tsv
+sample_1	test_input/Hinfluenzae/biotype/sample1.biotype.blast.tsv	test_input/Hinfluenzae/ariba_ftsI/sample1.ftsI.ariba.tsv	test_input/Hinfluenzae/hicap/sample1.hicap.tsv	test_input/Hinfluenzae/ariba_ftsI/ftsI_types_table.txt
+sample_2	test_input/empty_file.txt	test_input/empty_file.txt	test_input/empty_file.txt	test_input/empty_file.txt
+sample_3	test_input/nonexist_file.txt	test_input/nonexist_file.txt	test_input/nonexist_file.txt	test_input/nonexist_file.txt
+

test_input/Hinfluenzae/biotype/sample1.biotype.blast.tsv

@@ -0,0 +1,2 @@
+urease	HINF-2024-0115_7_215.085	89.703	1719	1719	1	1719	61211	59493	ATGGCATTAACAATTTCAAGAGCGCAATATGTAGCAACTTATGGCCCAACCGTTGGCGATAAAGTCCGTTTAGGCGATACCAATTTATGGGCAACTATTGAGCAAGATCTATTGACCAAAGGCGACGAGTGTAAATTTGGTGGCGGTAAAAGTGTACGCGATGGCATGGCTCAAAGTGGTACGGCAACTCGCGATAATCCAAATGTATTGGATTTTGTGATCACTAACGTGATGATCATTGATGCAAAATTAGGCATTATCAAAGCGGATATTGGGATTCGAGATGGTCGCATTGTGGGCATTGGTCAAGCAGGTAACCCAGATACGATGGATAATGTCACGCCAAATATGATTATCGGTGCTAGCACAGAAGTACATAACGGTGCACATTTAATTGCAACCGCTGGCGGTATTGATACACACATTCACTTTATTTGCCCTCAACAAGCACAGCATGCGATTGAAAGTGGCGTTACTACGTTAATTGGTGGCGGAACAGGCCCGGCTGACGGCACACACGCGACCACTTGCACACCAGGTGCGTGGTATATGGAGCGTATGTTCCAAGCGGCAGAAGCATTGCCTGTAAACGTAGGATTTTTTGGTAAAGGCAACTGTTCAACTTTAGATCCGCTACGCGAACAAATTGAAGCTGGCGCATTAGGTTTAAAAATCCACGAAGACTGGGGCGCAACGCCTGCAGTAATTGATTCGGCATTAAAAGTGGCAGATGAAATGGATATTCAAGTGGCAATCCACACCGACACTCTGAACGAAAGTGGCTTCTTAGAAGATACCATGAAAGCGATTGATGGACGTGTTATTCATACCTTCCACACGGAAGGAGCTGGTGGCGGTCATGCGCCAGATATCATTAAAGCAGCGATGTATCCAAACGTATTACCGGCTTCAACTAACCCAACTCGTCCGTTTACGAAAAACACTATCGATGAACATTTGGATATGTTGATGGTTTGCCATCATTTAGATAAACGCGTGCCAGAAGATGTAGCTTTTGCCGATAGCCGTATCCGTCCTGAAACTATTGCAGCAGAAGATATTTTGCATGATATGGGTGTTTTCTCGATTATGAGTTCAGACTCTCAAGCGATGGGGCGTATTGGCGAAGTCGTTATTCGTACATGGCAAACCGCAGATAAAATGAAAATGCAACGTGGCGAATTAGGCAATGAAGGAAACGATAACTTCCGTATTAAACGCTACATTGCGAAATATACCATCAATCCAGCGATTGCACACGGCATCTCGGATCATATTGGTTCATTAGAAGTGGGCAAAATTGCAGATATCGTGTTATGGAAACCGATGTTCTTTGGCGTAAAACCAGAAGTGGTAATTAAAAAAGGTTTTATTAGCTACGCAAAAATGGGCGATCCAAATGCCTCTATTCCAACACCACAACCAGTGTTCTACCGTCCAATGTACGGTGCACAAGGCTTAGCAACGGCACAAACTGCAGTTTTCTTTGTTTCACAAGCCGCTGAAAAAGCAGATATTCGTGCTAAATTCGGTTTACACAAAGAAACTATTGCGGTGAAAGGCTGCCGTAGTGTGAGTAAAAAAGATCTTGTTCATAATGATGCAACACCTGAAATTACAGTGGATCCAGAACGCTATGAAGTGCGTGTAGATGGTGAACTAATTACCTGTGAACCTGTGGATACGGTGCCATTGGGGCAACGGTATTTTATGTTCTAA	0.0	2194
+ODC	HINF-2024-0115_85_200.274	93.389	2163	2163	1	2163	12163	10001	ATGCCAAACTTAAAAATTGCATATAATCCAAAAGTTGAACAATATTTCTCTACAAATAGAGAATTAGTTGAAATTACCAAAACAGACTTTACTGATGTTGCAGCTATCATGTTGACATCAGGGGATGTAGGTGAATACCTTGAACGTATTCAAGCAACAAATTTTGGTATCCCAGTATTTGTTGTTCAAACTGAAGAAGAACAAGTTGATCCGAAATTCTATGATGCTATTTATCATATTCAAGATTTAAATGGTTATGACATTAAGCTTTATAGCCGTCAAATCGAAACTGCTGCAAGACTTTATGAAGAAAAAATGTTACCTCCATTCTTCAAAATGTTAAGTGAATATGTAGAAATGGGTAATATTGCTTTTGACTGTCCGGGACATCAAGGTGGTCAATACTACCGTAAACACCCAGCAGGTCGTTTCCTTTATGACTTCTACGGTGAAAACATTTTCCGTTCAGATATTTGTAATGCAGACGTGAAATTAGGTGACTTGTTAATTCACGAAGGTGCAGCTTGTGATGCACAAAAATATGCTGCTCAAGTATTCAATGCAGATAAAACTTACTTCGTATTAAATGGTACATCTTCTTCAAACAAAGTTGCATTAAACGCAGTACTTGCTCTGGGCGATTTAGTATTATTTGACCGTAATAACCATAAATCAAACCACCATGGTGCATTAATTCAAGCGGGTGCAACCCCAATTTACTTAGAAACTGCACGTAATCCATTTGGTTTCATTGGTGGTATCGATAGTCACTGCTTCGAAGAAGATTATTTGAAATCATTAATTAAAGAAGTGGCGCCTGAAAAATTAAACCAAAAACGTCCATTCCGTTTAGCCGTTATTCAATTAGGTACTTATGACGGTACAATTTATAACGCACGTCAAGTGGTAGATAAAATTGGTCATCTTTGTGACTACATCTTATTCGACTCTGCATGGGTAGGTTATGAACAATTTATTCCAATGATGAAAGACTGCTCTCCATTATTGCTTGAATTAAATGAAAATGACCCTGGTATTTTAGTGACTCAATCTGTTCATAAACAACAAGCAGGTTTCTCACAAACTTCACAAATTCACAAAAAAGATAAACACATTAAAGGTCAAGATCGTTATGTAAACCACAAACGTTTCAATAATGCCTTTATGTTACATGCGTCAACCAGTCCGTTCTATCCATTATTTGCGGCGTTAGATGTGAATGCAAAAATTCAAGGTAGCGAAGCGGGTCGTCGCTTATGGCATGAATGTGTGAAAGTAGGTATCGAAGCGCGTAAATTAGTGTTAAATCACTGTGAATTAATTCGTCCATTTATTCCAACCACAATTAAAGGTAAAAAATGGCAAGATTATGACACAGAAGAAATCGCAACTAATCTCGAATTCTTCAAATTTCACCCAACAGATACATGGCATAAATTTGAAGGCTATGCTGATGAACAATACTTCGTTGACCCTTGTAAATTCTTGCTTACCACACCAGGTATTAGCTTAGAAACAGGCGAATATGAAAAATTTGGTGTACCAGCAACTATTCTTGCTAACTACTTACGTGAAAACGGTATTATTCCGGAAAAATGTGACTTGAACTCAATCTTATTCTTGCTCACTCCGGCAGAAACCCTCACCAAAATGCAAACTTTGGTCGCTCAAATCGCCTTGTTTGAAAAACACATTAAACAAGACTCTTTATTAAAAGATGTATTGCCAACTGTGTATAAAAACAATGAAGACCGTTACAAAGACTATACTATCCGTCAATTATGCCAAGAAATGCATGACCTTTATGTAAGCCGCAATGTAAAACAACTTCAAAAAGACCTATTCCGTAAAGCAACATTACCGGAATATGCGTTAAATCCACACGATGCGAATATTGAATTCGTTCGTAACAAAGTTGAACTCGTTCCATTGACTGATATTGTTGGTCGTGTGGCTGCGGAAGGTGCATTACCTTATCCTCCAGGTGTGTTATGTGTGGTGCCTGGAGAAAGATGGAGTCCAACTGCACAAAAATACTTCCTTGCATTAGAAGAAGGTATCAACACATTACCTGGTTTCGCACCTGAAATCCAAGGGGTTTACTTACAAAAAGACCCTGATGGACGTACTCGTGCATATGGCTATGTTTTAACTGACTATTAA	0.0	3203

test_input/Hinfluenzae/hicap/sample1.hicap.tsv

@@ -0,0 +1,2 @@
+#isolate	predicted_serotype	attributes	genes_identified	locus_location	region_I_genes	region_II_genes	region_III_genes	IS1016_hits
+HINF-2024-0115	type_e	full_gene_complement,fragmented_locus	bexA,bexB,bexC,bexD,ecs1,ecs2,ecs3;ecs4,ecs5,ecs6,ecs7,ecs8,hcsA,hcsB	HINF-2024-0115_61_149.787:10271-19835;HINF-2024-0115_2_192.991:20-8457	4/4	8/8	2/2	1