ssi-analysis-result-parsers 0.0.9__py3-none-any.whl → 0.0.10__py3-none-any.whl

ssi_analysis_result_parsers/Ecoli_parser.py

@@ -0,0 +1,669 @@
+# AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/49_Ecoli_parser.ipynb.
+
+# %% auto 0
+__all__ = ['thresholds', 'samplesheet_path', 'output_dir', 'output_path', 'sample_sheet_df', 'sample_output_df', 'original_cols',
+           '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']
+
+# %% ../nbs/49_Ecoli_parser.ipynb 3
+import os
+import sys
+import pandas as pd
+from pathlib import Path
+import logging
+from datetime import datetime
+from typing import List, Dict
+from fastcore.script import call_parse
+
+# import functions from core module (optional, but most likely needed).
+from . import core
+
+# %% ../nbs/49_Ecoli_parser.ipynb 6
+thresholds = {
+    "stx": [98, 98],
+    "wzx": [98, 98],
+    "wzy": [98, 98],
+    "wzt": [98, 98],
+    "wzm": [98, 98],
+    "fliC": [90, 90],
+    "fli": [90, 90],
+    "eae": [95, 95],
+    "ehxA": [95, 95],
+    "other": [98, 98],
+}
+
+# %% ../nbs/49_Ecoli_parser.ipynb 9
+def setup_logging(log_dir: str, sample_name: str) -> None:
+    timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
+    os.makedirs(log_dir, exist_ok=True)
+    log_file = os.path.join(log_dir, f"{sample_name}_kma_fbi.log")
+
+    logger = logging.getLogger()
+    while logger.hasHandlers():
+        logger.removeHandler(logger.handlers[0])
+
+    logging.basicConfig(
+        filename=log_file,
+        filemode="a",
+        format="%(asctime)s - %(levelname)s - %(message)s",
+        level=logging.INFO,
+    )
+
+    console_handler = logging.StreamHandler(sys.stdout)
+    console_handler.setFormatter(logging.Formatter("%(message)s"))
+    logger.addHandler(console_handler)
+
+    logging.info(f"Logging started for {log_file}")
+
+# %% ../nbs/49_Ecoli_parser.ipynb 11
+def get_threshold(template_name: str, thresholds: Dict[str, List[int]]) -> List[int]:
+    """
+    Returns the coverage and identity threshold for a given gene.
+
+    Args:
+        template_name (str): Name of the template (gene) from the .res file.
+        thresholds (Dict[str, List[int]]): Dictionary of gene thresholds.
+
+    Returns:
+        List[int]: A list of two integers: [coverage_threshold, identity_threshold].
+    """
+    for key in thresholds:
+        if key in template_name:
+            return thresholds[key]
+    return thresholds["other"]
+
+
+def process_res_file(res_file_path: str) -> pd.DataFrame:
+    """
+    Reads and filters a KMA .res file based on predefined thresholds.
+
+    Args:
+        res_file_path (str): Path to the .res file.
+        thresholds (Dict[str, List[int]]): Gene-specific thresholds.
+
+    Returns:
+        pd.DataFrame: Filtered results DataFrame.
+    """
+    try:
+        res_df = pd.read_csv(res_file_path, sep="\t")
+    except FileNotFoundError:
+        raise FileNotFoundError(f"File not found: {res_file_path}")
+    except pd.errors.EmptyDataError:
+        raise ValueError(f"File is empty or not properly formatted: {res_file_path}")
+
+    required_columns = {"#Template", "Template_Coverage", "Query_Identity", "Depth"}
+    if not required_columns.issubset(res_df.columns):
+        raise ValueError(f"Missing expected columns in {res_file_path}")
+
+    res_df["threshold"] = res_df["#Template"].apply(
+        lambda x: get_threshold(x, thresholds)
+    )
+    res_df_filtered = res_df[
+        (res_df["Template_Coverage"] >= res_df["threshold"].apply(lambda x: x[0]))
+        & (res_df["Query_Identity"] >= res_df["threshold"].apply(lambda x: x[1]))
+    ]
+    return res_df_filtered
+
+# %% ../nbs/49_Ecoli_parser.ipynb 13
+class EcoliResults:
+    """
+    Object for holding and processing E. coli typing results.
+
+    This class stores summary typing data for multiple samples, provides utilities for per-sample processing, and export results in a tab-seperated format (.tsv).
+    """
+
+    # converts the sample results in dict to pandas df
+    def __init__(self, results_dict: dict):
+        """
+        Initializes the EcoliResults object with typing result data.
+
+        Args:
+            results_dict (dict): Dictionary where keys are sample names and values are summary result dictionaries.
+        """
+        self.results_dict = results_dict
+        self.results_df = pd.DataFrame.from_dict(
+            results_dict, orient="index"
+        ).reset_index(names="sample_name")
+
+    @staticmethod
+    def summarize_single_sample(
+        sample_name: str, res_path: str, verbose_flag: int = 1
+    ) -> dict:
+        """
+        Processes a single sample KMA .res file and returns a summary dictionary.
+
+        Args:
+            sample_name (str): Sample identifier.
+            res_path (str): Path to the sample's .res file.
+            verbose_flag (int, optional): Include verbose info if set to 1. Default is 1.
+
+        Returns:
+            Dict[str, str]: Summary values extracted from the .res file.
+        """
+        log_dir = "examples/Log"
+        setup_logging(log_dir, sample_name)
+
+        NA_string = "-"
+        output_data = {
+            "stx": NA_string,
+            "OH": NA_string,
+            "wzx": NA_string,
+            "wzy": NA_string,
+            "wzt": NA_string,
+            "wzm": NA_string,
+            "eae": NA_string,
+            "ehxA": NA_string,
+            "Other": NA_string,
+        }
+
+        try:
+            logging.info(f"Processing .res file: {res_path}")
+            filtered_df = process_res_file(res_path)
+        except Exception as e:
+            logging.error(f"Failed to process {res_path}: {e}")
+            return output_data
+
+        gene_map = {
+            "wzx": "wzx",
+            "wzy": "wzy",
+            "wzt": "wzt",
+            "wzm": "wzm",
+            "eae": "eae",
+            "ehxA": "ehxA",
+        }
+        toxin = "stx"
+        stx_alleles = set()
+        fli = NA_string
+        fliC = NA_string
+
+        for template in filtered_df["#Template"]:
+            parts = template.split("__")
+            if len(parts) < 3:
+                continue
+            gene, allele = parts[1], parts[2]
+
+            if gene in ["eae", "ehxA"]:
+                output_data[gene] = "Positive"
+            elif gene in gene_map:
+                output_data[gene] = allele
+            elif gene == "fliC":
+                fliC = allele
+            elif gene == "fli":
+                fli = allele
+            elif gene.startswith(toxin):
+                stx_alleles.add(allele)
+            elif gene not in thresholds:
+                output_data["Other"] = allele
+
+        if stx_alleles:
+            output_data[toxin] = ";".join(sorted(stx_alleles))
+
+        # serotype specific requirements
+        wzx, wzy, wzt, wzm = (
+            output_data["wzx"],
+            output_data["wzy"],
+            output_data["wzt"],
+            output_data["wzm"],
+        )
+        Otype = "-"
+        if (
+            wzx != NA_string
+            and wzy != NA_string
+            and wzx == wzy
+            and wzt == NA_string
+            and wzm == NA_string
+        ):
+            Otype = wzx
+            output_data["wzx"] = output_data["wzy"] = NA_string
+        elif (
+            wzt != NA_string
+            and wzm != NA_string
+            and wzt == wzm
+            and wzx == NA_string
+            and wzy == NA_string
+        ):
+            Otype = wzt
+            output_data["wzt"] = output_data["wzm"] = NA_string
+
+        Htype = fli if fli != NA_string else fliC
+        output_data["OH"] = f"{Otype};{Htype}"
+
+        # adding the additional depth, template coverage and query identity information
+        if verbose_flag == 1:
+            verbose_parts = []
+            for _, row in filtered_df.iterrows():
+                parts = row["#Template"].split("__")
+                if len(parts) >= 3:
+                    gene, allele = parts[1], parts[2]
+                    depth = row["Depth"]
+                    coverage = row["Template_Coverage"]
+                    identity = row["Query_Identity"]
+                    verbose_parts.append(
+                        f"{gene}_{allele}_{depth:.2f}_{coverage:.2f}_{identity:.2f}"
+                    )
+            output_data["verbose"] = ";".join(verbose_parts)
+
+        logging.info(f"Successfully processed sample: {sample_name}")
+        return output_data
+
+    @classmethod
+    def from_samplesheet(
+        cls,
+        samplesheet_path: Path,
+        verbose: int = 1,
+        results_base: str = "examples/Results/{sample_name}/kma/{sample_name}.res",
+    ) -> "EcoliResults":
+        """
+        Loads sample data from a samplesheet and summarizes each sample.
+
+        Args:
+            samplesheet_path (Path): Path to the samplesheet TSV file.
+            verbose (int, optional): Whether to include verbose output per sample. Default is 1.
+
+        Returns:
+            EcoliResults: An instance of the class populated with summaries for all samples.
+        """
+        df = pd.read_csv(samplesheet_path, sep="\t")
+        df.columns = df.columns.str.strip()
+        # print("I AM INSIDE FROM SAMPLESHEET")
+        # if "Illumina_read_files" in df.columns and ("read1" not in df.columns or "read2" not in df.columns):
+        #    df[["read1", "read2"]] = df["Illumina_read_files"].str.split(",", expand=True)
+
+        results_dict = {}
+        for idx, row in df.iterrows():
+            sample_name = row["sample_name"]
+            res_path = Path(
+                results_base.format(sample_name=sample_name)
+            )  # results_base / sample_name / "kma" / f"{sample_name}.res"
+            # print(f"The res path is : {res_path}")
+            summary = cls.summarize_single_sample(
+                sample_name, res_path, verbose_flag=verbose
+            )
+            results_dict[sample_name] = summary
+
+        # Convert to DataFrame
+        result_df = pd.DataFrame.from_dict(results_dict, orient="index").reset_index(
+            names="sample_name"
+        )
+
+        # Merge with original metadata
+        merged_df = df.merge(result_df, on="sample_name", how="left")
+
+        # Create and return object
+        obj = cls(results_dict)
+        obj.results_df = merged_df
+        return obj
+
+    def write_tsv(self, output_file: Path):
+        """
+        Writes the summarized typing results to a TSV file.
+
+        Args:
+            output_file (Path): Destination file path for the output table.
+        """
+        self.results_df.to_csv(output_file, sep="\t", index=False)
+
+    def __repr__(self):
+        """
+        Returns a concise summary of the results object.
+
+        Returns:
+            str: A string with sample and variable counts.
+        """
+        return f"<EcoliResults: {len(self.results_df)} samples, {len(self.results_df.columns)} variables>"
+
+# %% ../nbs/49_Ecoli_parser.ipynb 15
+@call_parse
+def ecoli_parser(
+    samplesheet_path: Path,  # Input samplesheet
+    output_file: Path = None,  # Path to output
+    verbose: int = 1,  # Verbosity,
+    results_base: str = "examples/Results/{sample_name}/kma/{sample_name}.res",  # Path template for .res files
+):
+    results = EcoliResults.from_samplesheet(
+        samplesheet_path, verbose=verbose, results_base=results_base
+    )
+    if output_file:
+        results.write_tsv(output_file)
+    else:
+        print(results.results_df)
+
+# %% ../nbs/49_Ecoli_parser.ipynb 17
+# | eval: true
+import pandas as pd
+from pathlib import Path
+import os
+
+# Define paths
+samplesheet_path = Path("test_input/Ecoli/samplesheet.tsv")
+output_dir = Path("test_output/Ecoli")
+
+# Create output directory
+if not output_dir.exists():
+    output_dir.mkdir(parents=True, exist_ok=True)
+
+output_path = output_dir / "KMA_cases_parser.tsv"
+
+# Assert input exists
+assert samplesheet_path.exists(), f"File does not exist: {samplesheet_path}"
+print(output_path)
+
+# try the ecoli parser to see if the wrangling functionality works
+try:
+    ecoli_parser(
+        samplesheet_path=samplesheet_path,
+        output_file=output_path,
+        verbose=1,
+        results_base="test_input/Ecoli/{sample_name}.res",
+    )
+except Exception as e:
+    raise AssertionError(f"Parser execution failed: {e}")
+
+# compare the output with the expected results based on input to ensure correct wrangling
+
+# read the created output files and check the information
+sample_sheet_df = pd.read_csv(samplesheet_path, sep="\t")
+sample_output_df = pd.read_csv(output_path, sep="\t")
+
+### Test case 1. Check if the datastructure is correct
+original_cols = sample_sheet_df.columns.tolist()
+output_cols = sample_output_df.columns.tolist()
+output_initial_cols = sample_output_df.columns[: len(original_cols)].tolist()
+output_specific_cols = sample_output_df.columns[len(original_cols) :].tolist()
+
+assert (
+    original_cols == output_initial_cols
+), f"Mismatch in first columns:\nExpected: {original_cols}\nGot: {output_initial_cols}"
+
+assert output_specific_cols
+
+### Test case 2. Check sample ERR3528110 which is correctly believed to be e.coli and ensure datawrangling does as expected
+ERR3528110_res_path = "test_input/Ecoli/ERR3528110.res"
+ERR3528110_input_df = pd.read_csv(ERR3528110_res_path, sep="\t")
+
+ERR3528110_row = (
+    sample_output_df[sample_output_df["sample_name"] == "ERR3528110"]
+    .iloc[:, len(original_cols) : len(output_cols)]
+    .iloc[0]
+)
+
+# extract the original genes from the res
+gene_hits = ERR3528110_input_df["#Template"].tolist()
+
+parsed_hits = []
+
+for hit in gene_hits:
+    parts = hit.split("__")
+    assert (
+        len(parts) != 3
+    ), f"Unexpected KMA result format in: '{hit}'. Expected at least 3 '__' parts (e.g., ref__gene__allele) as off ecoli fbi 24-04-2025."
+    gene, allele = parts[1], parts[2]
+    parsed_hits.append((gene, allele))
+
+# Extract OH genes
+O_gene_alleles = {
+    gene: allele for gene, allele in parsed_hits if gene in {"wzx", "wzy", "wzt", "wzm"}
+}
+H_gene_alleles = {
+    gene: allele for gene, allele in parsed_hits if gene in {"fli", "fliC"}
+}
+
+O_type = ERR3528110_row["OH"].split(";")[0]
+H_type = ERR3528110_row["OH"].split(";")[1]
+
+O_gene_keys = set(O_gene_alleles.keys())
+H_gene_keys = set(H_gene_alleles.keys())
+
+O_genes_no = len(O_gene_keys)
+H_genes_no = len(H_gene_keys)
+
+# O typing scenarios
+# Case 1: wzx/wzy match
+if O_gene_keys == {"wzx", "wzy"} and O_gene_alleles["wzx"] == O_gene_alleles["wzy"]:
+    expected_otype = O_gene_alleles["wzx"]
+    assert O_type == expected_otype, f"Expected OH '{expected_otype}', got '{O_type}'"
+    # wzx/wzy should be suppressed
+    assert ERR3528110_row["wzx"] == "-", "wzx column should be '-' when OH is used"
+    assert ERR3528110_row["wzy"] == "-", "wzy column should be '-' when OH is used"
+    # print(f"O-type correctly assigned from matching wzx/wzy: {O_type}")
+
+# Case 2: wzt/wzm match
+elif O_gene_keys == {"wzt", "wzm"} and O_gene_alleles["wzt"] == O_gene_alleles["wzm"]:
+    expected_otype = O_gene_alleles["wzt"]
+    assert O_type == expected_otype, f"Expected OH '{expected_otype}', got '{O_type}'"
+    assert ERR3528110_row["wzt"] == "-", "wzt column should be '-' when OH is used"
+    assert ERR3528110_row["wzm"] == "-", "wzm column should be '-' when OH is used"
+    # print(f"O-type correctly assigned from matching wzt/wzm: {O_type}")
+
+# Case 3: Conflict (≥3 genes, or 2 mismatched genes)
+elif O_genes_no >= 3 or (
+    (O_gene_keys == {"wzx", "wzy"} and O_gene_alleles["wzx"] != O_gene_alleles["wzy"])
+    or (
+        O_gene_keys == {"wzt", "wzm"} and O_gene_alleles["wzt"] != O_gene_alleles["wzm"]
+    )
+):
+    assert O_type == "-", f"Expected OH = '-' due to conflict, got: '{O_type}'"
+    for gene in O_gene_keys:
+        assert (
+            ERR3528110_row[gene] == O_gene_alleles[gene]
+        ), f"{gene} column should contain '{O_gene_alleles[gene]}'"
+    # print("Conflict in O-typing correctly led to OH = '-' and individual gene columns retained.")
+
+# H typing scenarios
+
+# Case 1: If fli is present it will always take precedence over fliC
+if H_gene_keys == {"fli"}:
+    expected_htype = H_gene_alleles["fli"]
+    assert (
+        H_type == expected_htype
+    ), f"Expected OH '{expected_htype}' from 'fli', got '{H_type}'"
+
+# Case 2: only if fliC is the sole gene it is used
+elif H_gene_keys == {"fliC"}:
+    expected_htype = H_gene_alleles["fliC"]
+    assert (
+        H_type == expected_htype
+    ), f"Expected OH '{expected_htype}' from 'fliC', got '{H_type}'"
+
+# Case 3: if none exist the H type remains empty
+else:
+    assert H_type == "-", f"Expected H-type '-', but got '{H_type}'"
+
+### Test case 3. Check sample ERR14229029 which is believed to be e.coli in the samplesheet is empty, as a result of being erroneously classified as e.coli
+
+ERR14229029_row = (
+    sample_output_df[sample_output_df["sample_name"] == "ERR14229029"]
+    .iloc[:, len(original_cols) : len(output_cols)]
+    .iloc[0]
+)
+
+ERR14229029_expected_values = [
+    "-",
+    "-;-",
+    "-",
+    "-",
+    "-",
+    "-",
+    "-",
+    "-",
+    "-",
+    float("nan"),
+]
+ERR14229029_values = [ERR14229029_row[col] for col in output_specific_cols]
+
+for col, actual, expected in zip(
+    output_specific_cols, ERR14229029_values, ERR14229029_expected_values
+):
+    if pd.isna(expected):
+        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/Spyogenes_parser.py

@@ -193,7 +193,6 @@ def extract_emm_type(emm_blast_tsv: Path):
                         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:

ssi_analysis_result_parsers/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.9"
+__version__ = "0.0.10"

ssi_analysis_result_parsers/_modidx.py

@@ -5,7 +5,27 @@ d = { 'settings': { 'branch': 'main',
                 'doc_host': 'https://thej-ssi.github.io',
                 'git_url': 'https://github.com/thej-ssi/ssi_analysis_result_parsers',
                 'lib_path': 'ssi_analysis_result_parsers'},
-  'syms': { 'ssi_analysis_result_parsers.Legionella_parser': { 'ssi_analysis_result_parsers.Legionella_parser.LegionellaResults': ( 'legionella_parser.html#legionellaresults',
+  'syms': { 'ssi_analysis_result_parsers.Ecoli_parser': { 'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults': ( 'ecoli_parser.html#ecoliresults',
+                                                                                                                     'ssi_analysis_result_parsers/Ecoli_parser.py'),
+                                                          'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults.__init__': ( 'ecoli_parser.html#ecoliresults.__init__',
+                                                                                                                              'ssi_analysis_result_parsers/Ecoli_parser.py'),
+                                                          'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults.__repr__': ( 'ecoli_parser.html#ecoliresults.__repr__',
+                                                                                                                              'ssi_analysis_result_parsers/Ecoli_parser.py'),
+                                                          'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults.from_samplesheet': ( 'ecoli_parser.html#ecoliresults.from_samplesheet',
+                                                                                                                                      'ssi_analysis_result_parsers/Ecoli_parser.py'),
+                                                          'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults.summarize_single_sample': ( 'ecoli_parser.html#ecoliresults.summarize_single_sample',
+                                                                                                                                             'ssi_analysis_result_parsers/Ecoli_parser.py'),
+                                                          'ssi_analysis_result_parsers.Ecoli_parser.EcoliResults.write_tsv': ( 'ecoli_parser.html#ecoliresults.write_tsv',
+                                                                                                                               'ssi_analysis_result_parsers/Ecoli_parser.py'),
+                                                          'ssi_analysis_result_parsers.Ecoli_parser.ecoli_parser': ( 'ecoli_parser.html#ecoli_parser',
+                                                                                                                     'ssi_analysis_result_parsers/Ecoli_parser.py'),
+                                                          'ssi_analysis_result_parsers.Ecoli_parser.get_threshold': ( 'ecoli_parser.html#get_threshold',
+                                                                                                                      'ssi_analysis_result_parsers/Ecoli_parser.py'),
+                                                          'ssi_analysis_result_parsers.Ecoli_parser.process_res_file': ( 'ecoli_parser.html#process_res_file',
+                                                                                                                         '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.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/Legionella_parser.py'),

{ssi_analysis_result_parsers-0.0.9.dist-info → ssi_analysis_result_parsers-0.0.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ssi_analysis_result_parsers
-Version: 0.0.9
+Version: 0.0.10
 Summary: TODO
 Home-page: https://github.com/thej-ssi/ssi_analysis_result_parsers
 Author: Thor Bech Johannesen

{ssi_analysis_result_parsers-0.0.9.dist-info → ssi_analysis_result_parsers-0.0.10.dist-info}/RECORD

@@ -1,16 +1,20 @@
+ssi_analysis_result_parsers/Ecoli_parser.py,sha256=lKNnx27KqxpX3yv1RAP-sBATMGf9yjfSs4-d50mR2cA,22704
 ssi_analysis_result_parsers/Legionella_parser.py,sha256=nBOPrelzCMh8IMEDje6jtU9sz92sEyuxddBe0MntTfo,6879
-ssi_analysis_result_parsers/Spyogenes_parser.py,sha256=AaA-63AWbRdjkqdZQahGktwDObsSS9KxDwroftzoDiw,12804
-ssi_analysis_result_parsers/__init__.py,sha256=46Yjk3fz9o8aTN8E95McnzpJcjGzVJmHmQqUZ5mXzfc,22
-ssi_analysis_result_parsers/_modidx.py,sha256=kz1oGnDbstzvo_tNuFiX5wkhfhNmiqSiCkwBnzplRU0,14895
+ssi_analysis_result_parsers/Spyogenes_parser.py,sha256=Cjibp7iKGofjSp-igm-jmjBVkQ6-zxYQWVSZT-Vx3Fo,12731
+ssi_analysis_result_parsers/__init__.py,sha256=-nNlMKS9nph3FR78_ZG9RGKrbxseeNp2K6nMr0pVGaU,23
+ssi_analysis_result_parsers/_modidx.py,sha256=JAUPTOicf6tKcLhA8DOvsehlZxy6LDPxQDlootV_InE,18281
 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-0.0.9.dist-info/licenses/LICENSE,sha256=p6aTb6QIfqyZ2Uux2VjV4F2zthdUSHZOjB4mfwGc7fo,1094
+ssi_analysis_result_parsers-0.0.10.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/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
@@ -34,8 +38,9 @@ test_input/blast_parser/gene_presence_absence_test.tsv,sha256=qCvMkBC-1GuXx83RDh
 test_output/output_with_sample_name.tsv,sha256=NQG7WaxczuWCCsX2a9MUxCCYpbuAirz9gw08OLdEdUo,41
 test_output/test.tsv,sha256=6DGzarXMkUP03Z58vZimc-gu1K2k84zxZLWWF2HROCg,277
 test_output/test_batch_output.tsv,sha256=6DGzarXMkUP03Z58vZimc-gu1K2k84zxZLWWF2HROCg,277
-ssi_analysis_result_parsers-0.0.9.dist-info/METADATA,sha256=gpcbUHkicHpg_derxQTQetNGZOoj5X5mPbcxI_lElm0,2765
-ssi_analysis_result_parsers-0.0.9.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-ssi_analysis_result_parsers-0.0.9.dist-info/entry_points.txt,sha256=noBLlB4hLmYcqns7KdQPVURO27kZ_zWMsPHYkRlBGEE,631
-ssi_analysis_result_parsers-0.0.9.dist-info/top_level.txt,sha256=3q56bBc2Wv2a6ZQ1l_9m66vot2-Qu6tM9tDr3QQ8auM,81
-ssi_analysis_result_parsers-0.0.9.dist-info/RECORD,,
+test_output/Ecoli/KMA_cases_parser.tsv,sha256=Wf3JkSppRN5AK2zRJmFQlwVfCMyJfgyyBpTjb1sK6Uw,586
+ssi_analysis_result_parsers-0.0.10.dist-info/METADATA,sha256=BZSffWWanmoRU6UPhhJl6jc1pBomIvjyX79m-H39DAI,2766
+ssi_analysis_result_parsers-0.0.10.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+ssi_analysis_result_parsers-0.0.10.dist-info/entry_points.txt,sha256=1btBaEDONU_OZlGK4iXe0-my25NFtup33MfYFS-Oj24,705
+ssi_analysis_result_parsers-0.0.10.dist-info/top_level.txt,sha256=dhzhsC8l7PYeBYNT8JzHPz3BriLAw3llVo0jHn175WI,90
+ssi_analysis_result_parsers-0.0.10.dist-info/RECORD,,

{ssi_analysis_result_parsers-0.0.9.dist-info → ssi_analysis_result_parsers-0.0.10.dist-info}/entry_points.txt

@@ -3,6 +3,7 @@ blast_parser_allele_matches = ssi_analysis_result_parsers.blast_parser:allele_ma
 blast_parser_presence_absence = ssi_analysis_result_parsers.blast_parser:presence_absence
 get_Spyogenes_results = ssi_analysis_result_parsers.Spyogenes_parser:Spyogenes_parser
 get_Spyogenes_results_batch = ssi_analysis_result_parsers.Spyogenes_parser:Spyogenes_batch_parser
+get_ecoli_results = ssi_analysis_result_parsers.Ecoli_parser:ecoli_parser
 get_leg_results = ssi_analysis_result_parsers.Legionella_parser:legionella_parser
 get_leg_results_batch = ssi_analysis_result_parsers.Legionella_parser:legionella_batch_parser
 

{ssi_analysis_result_parsers-0.0.9.dist-info → ssi_analysis_result_parsers-0.0.10.dist-info}/top_level.txt

@@ -1,5 +1,6 @@
 _proc
 config
+examples
 input
 nbs
 output

test_input/Ecoli/ERR14229029.res

@@ -0,0 +1 @@
+#Template	Score	Expected	Template_length	Template_Identity	Template_Coverage	Query_Identity	Query_Coverage	Depth	q_value	p_value

test_input/Ecoli/ERR3528110.res

@@ -0,0 +1,4 @@
+#Template	Score	Expected	Template_length	Template_Identity	Template_Coverage	Query_Identity	Query_Coverage	Depth	q_value	p_value
+1__wzx__O6__AJ426045	   20056	     153	    1257	   99.92	  100.00	   99.92	  100.00	   16.07	19601.01	1.0e-26
+2__wzy__O6__AJ426423	   23540	     159	    1344	  100.00	  100.00	  100.00	  100.00	   17.35	23065.87	1.0e-26
+5__fliC__H1__AB028471	  107030	      73	    1788	  100.00	  100.00	  100.00	  100.00	   62.14	106810.34	1.0e-26

test_input/Ecoli/samplesheet.tsv

@@ -0,0 +1,3 @@
+sample_name	Illumina_read_files	Nanopore_read_file	assembly_file	organism	variant	notes
+ERR3528110	examples/Dataset/reads/ERR3528110_1.fastq.gz,examples/Dataset/reads/ERR3528110_2.fastq.gz	Na	examples/Dataset/assemblies/ERR3528110.fasta	E.coli	Na	Na
+ERR14229029	examples/Dataset/reads/ERR14229029_1.fastq.gz,examples/Dataset/reads/ERR14229029_2.fastq.gz	Na	examples/Dataset/assemblies/ERR14229029.fasta	E.coli	Na	Na

test_output/Ecoli/KMA_cases_parser.tsv

@@ -0,0 +1,3 @@
+sample_name	Illumina_read_files	Nanopore_read_file	assembly_file	organism	variant	notes	stx	OH	wzx	wzy	wzt	wzm	eae	ehxA	Other	verbose
+ERR3528110	examples/Dataset/reads/ERR3528110_1.fastq.gz,examples/Dataset/reads/ERR3528110_2.fastq.gz	Na	examples/Dataset/assemblies/ERR3528110.fasta	E.coli	Na	Na	-	O6;H1	-	-	-	-	-	-	-	wzx_O6_16.07_100.00_99.92;wzy_O6_17.35_100.00_100.00;fliC_H1_62.14_100.00_100.00
+ERR14229029	examples/Dataset/reads/ERR14229029_1.fastq.gz,examples/Dataset/reads/ERR14229029_2.fastq.gz	Na	examples/Dataset/assemblies/ERR14229029.fasta	E.coli	Na	Na	-	-;-	-	-	-	-	-	-	-