mgnify-pipelines-toolkit 1.0.9__tar.gz → 1.1.1__tar.gz

{mgnify_pipelines_toolkit-1.0.9 → mgnify_pipelines_toolkit-1.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mgnify_pipelines_toolkit
-Version: 1.0.9
+Version: 1.1.1
 Summary: Collection of scripts and tools for MGnify pipelines
 Author-email: MGnify team <metagenomics-help@ebi.ac.uk>
 License: Apache Software License 2.0
@@ -8,7 +8,7 @@ Keywords: bioinformatics,pipelines,metagenomics
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Operating System :: OS Independent
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: biopython>=1.85

{mgnify_pipelines_toolkit-1.0.9 → mgnify_pipelines_toolkit-1.1.1}/mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py

@@ -427,7 +427,7 @@ def retrieve_regions(
                     new_value.append(region)
             if not new_value:
                 models_to_remove.append(model)
-            if len(new_value) < MIN_SEQ_COUNT:
+            elif len(new_value) < MIN_SEQ_COUNT:
                 models_to_remove.append(model)
             multiregion_matches[model] = new_value
 

{mgnify_pipelines_toolkit-1.0.9/mgnify_pipelines_toolkit/analysis/shared → mgnify_pipelines_toolkit-1.1.1/mgnify_pipelines_toolkit/analysis/amplicon}/study_summary_generator.py

@@ -257,7 +257,7 @@ def organise_study_summaries(all_study_summaries: List[str]) -> defaultdict[List
 @cli.command(
     "summarise",
     options_metavar="-r <runs> -a <analyses_dir> -p <output_prefix>",
-    short_help="Generate study-level analysis summaries.",
+    short_help="Generate study-level summaries of amplicon analysis results.",
 )
 @click.option(
     "-r",
@@ -327,7 +327,7 @@ def summarise_analyses(
 @cli.command(
     "merge",
     options_metavar="-a <analyses_dir> -p <output_prefix>",
-    short_help="Merge multiple study-level analysis summaries.",
+    short_help="Merge multiple study-level summaries of amplicon analysis.",
 )
 @click.option(
     "-a",

mgnify_pipelines_toolkit-1.1.1/mgnify_pipelines_toolkit/analysis/assembly/study_summary_generator.py

@@ -0,0 +1,605 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+# Copyright 2025 EMBL - European Bioinformatics Institute
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import click
+from functools import reduce
+import glob
+import logging
+from pathlib import Path
+from typing import Literal
+
+import pandas as pd
+
+from mgnify_pipelines_toolkit.schemas.schemas import (
+    CompletedAnalysisSchema,
+    TaxonSchema,
+    GOSummarySchema,
+    InterProSummarySchema,
+    KOSummarySchema,
+    SanntisSummarySchema,
+    AntismashSummarySchema,
+    PFAMSummarySchema,
+    KEGGModulesSummarySchema,
+    GOStudySummarySchema,
+    InterProStudySummarySchema,
+    TaxonomyStudySummarySchema,
+    KOStudySummarySchema,
+    SanntisStudySummarySchema,
+    AntismashStudySummarySchema,
+    PFAMStudySummarySchema,
+    KEGGModulesStudySummarySchema,
+    validate_dataframe,
+)
+
+logging.basicConfig(
+    level=logging.DEBUG, format="%(asctime)s - %(levelname)s - %(message)s"
+)
+
+# Keys are the original column names in the input files,
+# values are the standardised column names used in the generated study summary files
+# Note: "Count" or "count" column should be excluded
+GO_COLUMN_NAMES = {
+    "go": "GO",
+    "term": "description",
+    "category": "category",
+}
+
+INTERPRO_COLUMN_NAMES = {
+    "interpro_accession": "IPR",
+    "description": "description",
+}
+
+SANNTIS_COLUMN_NAMES = {
+    "nearest_mibig": "nearest_mibig",
+    "nearest_mibig_class": "nearest_mibig_class",
+    "description": "description",
+}
+
+ANTISMASH_COLUMN_NAMES = {
+    "label": "label",
+    "description": "description",
+}
+
+KEGG_COLUMN_NAMES = {
+    "ko": "KO",
+    "description": "description",
+}
+
+PFAM_COLUMN_NAMES = {
+    "pfam": "PFAM",
+    "description": "description",
+}
+
+KEGG_MODULES_COLUMN_NAMES = {
+    "module_accession": "module_accession",
+    "pathway_name": "pathway_name",
+    "pathway_class": "pathway_class",
+}
+
+# this mapping allows using 'for' cycle later to process all summary types in one way
+SUMMARY_TYPES_MAP = {
+    "go": {
+        "folder": "functional-annotation/go",
+        "column_names": GO_COLUMN_NAMES,
+        "schema": GOSummarySchema,
+        "study_schema": GOStudySummarySchema,
+    },
+    "goslim": {
+        "folder": "functional-annotation/go",
+        "column_names": GO_COLUMN_NAMES,
+        "schema": GOSummarySchema,
+        "study_schema": GOStudySummarySchema,
+    },
+    "interpro": {
+        "folder": "functional-annotation/interpro",
+        "column_names": INTERPRO_COLUMN_NAMES,
+        "schema": InterProSummarySchema,
+        "study_schema": InterProStudySummarySchema,
+    },
+    "ko": {
+        "folder": "functional-annotation/kegg",
+        "column_names": KEGG_COLUMN_NAMES,
+        "schema": KOSummarySchema,
+        "study_schema": KOStudySummarySchema,
+    },
+    "sanntis": {
+        "folder": "pathways-and-systems/sanntis",
+        "column_names": SANNTIS_COLUMN_NAMES,
+        "schema": SanntisSummarySchema,
+        "study_schema": SanntisStudySummarySchema,
+    },
+    "antismash": {
+        "folder": "pathways-and-systems/antismash",
+        "column_names": ANTISMASH_COLUMN_NAMES,
+        "schema": AntismashSummarySchema,
+        "study_schema": AntismashStudySummarySchema,
+    },
+    "pfam": {
+        "folder": "functional-annotation/pfam",
+        "column_names": PFAM_COLUMN_NAMES,
+        "schema": PFAMSummarySchema,
+        "study_schema": PFAMStudySummarySchema,
+    },
+    "kegg_modules": {
+        "folder": "pathways-and-systems/kegg-modules",
+        "column_names": KEGG_MODULES_COLUMN_NAMES,
+        "schema": KEGGModulesSummarySchema,
+        "study_schema": KEGGModulesStudySummarySchema,
+    },
+}
+
+# The taxonomy file is a tab-separated file without any header
+# containing of following columns:
+TAXONOMY_COLUMN_NAMES = [
+    "Count",
+    "Superkingdom",
+    "Kingdom",
+    "Phylum",
+    "Class",
+    "Order",
+    "Family",
+    "Genus",
+    "Species",
+]
+
+OUTPUT_SUFFIX = "summary.tsv"
+
+
+@click.group()
+def cli():
+    pass
+
+
+def check_files_exist(file_list: list[Path]) -> None:
+    """
+    Check that all files in the given list exist on disk.
+
+    :param file_list: List of file paths to check.
+    :raises FileNotFoundError: If any file does not exist.
+    """
+    missing_files = [str(path) for path in file_list if not path.is_file()]
+    if missing_files:
+        raise FileNotFoundError(
+            f"The following required files are missing: {', '.join(missing_files)}"
+        )
+
+
+def generate_taxonomy_summary(
+    file_dict: dict[str, Path],
+    output_file_name: str,
+    outdir: Path = None,
+) -> None:
+    """
+    Generate a combined study-level taxonomic classification summary from multiple input
+    assembly-level summary files.
+
+    :param file_dict: Dictionary mapping assembly accession to its taxonomy file.
+    :param output_file_name: Output path for the output summary file.
+    :param outdir: Optional output directory for the results.
+
+    Example of the taxonomy file:
+    23651	sk__Bacteria
+    4985	sk__Archaea	k__Thermoproteati	p__Nitrososphaerota
+    882	sk__Archaea	k__Nanobdellati	p__	c__	o__	f__	g__	s__Candidatus Pacearchaeota archaeon
+    """
+    check_files_exist(list(file_dict.values()))
+
+    tax_dfs = []
+    for assembly_acc, path in file_dict.items():
+        df = pd.read_csv(path, sep="\t", names=TAXONOMY_COLUMN_NAMES).fillna("")
+
+        # Note: schema validation will fail if the taxonomy file is empty
+        df = validate_dataframe(df, TaxonSchema, str(path))
+
+        # Combine all taxonomic ranks in the classification into a single string
+        df["full_taxon"] = (
+            df[TAXONOMY_COLUMN_NAMES[1:]].agg(";".join, axis=1).str.strip(";")
+        )
+
+        # Create a new DataFrame with taxonomy as index and count as the only column
+        result = df[["Count", "full_taxon"]].set_index("full_taxon")
+        result.columns = [assembly_acc]
+        tax_dfs.append(result)
+
+    summary_df = pd.concat(tax_dfs, axis=1)
+    summary_df = summary_df.fillna(0).astype(int).sort_index()
+
+    outfile = output_file_name
+    if outdir:
+        outfile = outdir / output_file_name
+
+    summary_df.to_csv(outfile, sep="\t", index_label="taxonomy")
+
+
+def generate_functional_summary(
+    file_dict: dict[str, Path],
+    column_names: dict[str, str],
+    output_prefix: str,
+    label: Literal[
+        "go", "goslim", "interpro", "ko", "sanntis", "antismash", "pfam", "kegg_modules"
+    ],
+    outdir: Path = None,
+) -> None:
+    """
+    Generate a combined study-level functional annotation summary from multiple input
+    assembly-level summary files.
+
+    :param file_dict: Dictionary mapping assembly accession to its summary file path.
+    :param column_names: Dictionary mapping original column names to standard column names.
+    :param output_prefix: Prefix for the output summary file.
+    :param label: Label for the functional annotation type
+    (expected one of ["go", "goslim", "interpro", "ko", "sanntis", "antismash", "pfam", "kegg_modules"]).
+    :param outdir: Optional output directory for the results.
+
+    In the input files, column orders may vary, but the following columns are expected:
+    GO summary input file:
+    go	term	category	count
+    GO:0016020	membrane	cellular_component	30626
+    GO:0005524	ATP binding	molecular_function	30524
+
+    InterPro summary input file:
+    interpro_accession	description	count
+    IPR036291	NAD(P)-binding domain superfamily	16503
+    IPR019734	Tetratricopeptide repeat	14694
+
+    KEGG summary input file:
+    ko      description	count
+    K01552  energy-coupling factor transport system ATP-binding protein [EC:7.-.-.-]	562
+    K18889  ATP-binding cassette, subfamily B, multidrug efflux pump	537
+    K15497  molybdate/tungstate transport system ATP-binding protein [EC:7.3.2.5 7.3.2.6]	517
+
+    Sanntis summary input file:
+    nearest_mibig	nearest_mibig_class	description	count
+    BGC0000787	Saccharide	Carbohydrate-based natural products (e.g., aminoglycoside antibiotics)	1
+    BGC0000248	Polyketide	Built from iterative condensation of acetate units derived from acetyl-CoA	3
+    BGC0001327	NRP Polyketide	Nonribosomal Peptide Polyketide	2
+
+    Antismash summary input file:
+    label	description	count
+    terpene	Terpene	16
+    betalactone	Beta-lactone containing protease inhibitor	8
+    T1PKS	Type I PKS (Polyketide synthase)	3
+
+    PFAM summary input file:
+    pfam	description	count
+    PF00265	Thymidine kinase	457
+    PF01852	START domain	368
+    PF13756	Stimulus-sensing domain	397
+
+    KEGG modules summary input file:
+    module_accession	completeness	pathway_name	pathway_class	matching_ko	missing_ko
+    M00986	100.0	Sulfur reduction, sulfur => sulfide	Pathway modules; Energy metabolism; Sulfur metabolism	K18367
+    M00163	83.33	Photosystem I	Pathway modules; Energy metabolism; Photosynthesis	K02689,K02690,K02691,K02692,K02694	K02693
+    M00615	50.0	Nitrate assimilation	Signature modules; Module set; Metabolic capacity	K02575	M00531
+    """
+    check_files_exist(list(file_dict.values()))
+
+    output_file_name = f"{output_prefix}_{label}_{OUTPUT_SUFFIX}"
+
+    original_col_names = list(column_names.keys())
+    renamed_col_names = list(column_names.values())
+    value_col_name = "completeness" if label == "kegg_modules" else "count"
+
+    dfs = []
+    for assembly_acc, filepath in file_dict.items():
+        try:
+            df = pd.read_csv(filepath, sep="\t")
+        except pd.errors.EmptyDataError:
+            logging.warning(f"File {filepath.resolve()} is empty. Skipping.")
+            continue
+
+        schema = SUMMARY_TYPES_MAP[label]["schema"]
+        df = validate_dataframe(df, schema, str(filepath))
+
+        # Extract only relevant columns
+        df = df[original_col_names + [value_col_name]].copy()
+
+        # Rename columns: metadata columns are renamed according to column_names dict, "count"/"completeness" -> assembly acc
+        df.rename(columns={**column_names, value_col_name: assembly_acc}, inplace=True)
+        dfs.append(df)
+
+    if not dfs:
+        logging.warning(
+            f"No valid files with functional annotation summary were found. Skipping creation of {output_file_name}."
+        )
+        return
+
+    # Merge all dataframes on the renamed metadata columns
+    merged_df = reduce(
+        lambda left, right: pd.merge(left, right, on=renamed_col_names, how="outer"),
+        dfs,
+    )
+
+    # Fill missing values appropriately, convert completeness percentages to float, counts to integers
+    value_columns = [col for col in merged_df.columns if col not in renamed_col_names]
+    fill_value = 0.0 if label == "kegg_modules" else 0
+    dtype = float if label == "kegg_modules" else int
+    merged_df[value_columns] = merged_df[value_columns].fillna(fill_value).astype(dtype)
+
+    # Reorder columns: merge keys first, then sorted assembly accessions
+    merged_df = merged_df[renamed_col_names + sorted(value_columns)]
+
+    outfile = output_file_name
+    if outdir:
+        outfile = outdir / output_file_name
+
+    merged_df.to_csv(outfile, sep="\t", index=False)
+
+
+@cli.command(
+    "summarise",
+    options_metavar="-a <assemblies> -s <study_dir> -p <output_prefix>",
+    short_help="Generate study-level summaries for assembly analysis results.",
+)
+@click.option(
+    "-a",
+    "--assemblies",
+    required=True,
+    help="CSV file containing successful analyses generated by the pipeline",
+    type=click.Path(exists=True, path_type=Path, dir_okay=False),
+)
+@click.option(
+    "-s",
+    "--study_dir",
+    required=True,
+    help="Input directory to where all the individual analyses subdirectories for summarising",
+    type=click.Path(exists=True, path_type=Path, file_okay=False),
+)
+@click.option(
+    "-p",
+    "--output_prefix",
+    required=True,
+    help="Prefix for generated summary files",
+    type=str,
+)
+@click.option(
+    "-o",
+    "--outdir",
+    required=False,
+    help="Directory for the output files, by default it will use the current working directory.",
+    type=click.Path(exists=True, path_type=Path, file_okay=False),
+)
+def summarise_analyses(
+    assemblies: Path, study_dir: Path, output_prefix: str, outdir: Path
+) -> None:
+    """
+    Generate study-level summaries for successfully proccessed assemblies.
+
+    :param assemblies: Path to a file listing completed assembly accessions and their status.
+    :param study_dir: Path to the directory containing analysis results for each assembly.
+    :param output_prefix: Prefix for the generated summary files.
+    """
+    logging.info(f"Reading assembly list from {assemblies.resolve()}")
+    assemblies_df = pd.read_csv(assemblies, names=["assembly", "status"])
+    CompletedAnalysisSchema(assemblies_df)
+    assembly_list = assemblies_df["assembly"].tolist()
+    logging.info("Assembly list was read successfully.")
+
+    def get_file_paths(subdir: str, filename_template: str) -> dict[str, Path]:
+        """
+        Construct file paths for each assembly given a subdirectory and filename template.
+        Template must contain {acc} as a placeholder.
+        """
+        return {
+            acc: study_dir / acc / subdir / filename_template.format(acc=acc)
+            for acc in assembly_list
+        }
+
+    logging.info("Start processing of assembly-level summaries.")
+
+    logging.info(
+        "Generating taxonomy summary from assembly-level summaries <accession>.krona.txt"
+    )
+    generate_taxonomy_summary(
+        get_file_paths("taxonomy", "{acc}.krona.txt.gz"),
+        f"{output_prefix}_taxonomy_{OUTPUT_SUFFIX}",
+        outdir=outdir,
+    )
+
+    for summary_type, config in SUMMARY_TYPES_MAP.items():
+        logging.info(
+            f"Generating study-level {summary_type.capitalize()} summary from file <accession>_{summary_type}_summary.tsv.gz"
+        )
+        generate_functional_summary(
+            get_file_paths(config["folder"], f"{{acc}}_{summary_type}_summary.tsv.gz"),
+            config["column_names"],
+            output_prefix,
+            summary_type,
+            outdir=outdir,
+        )
+    logging.info("Assembly-level summaries were generated successfully.")
+    logging.info("Done.")
+
+
+@cli.command(
+    "merge",
+    options_metavar="-a <study_dir> -p <output_prefix>",
+    short_help="Merge multiple study-level summaries of assembly analysis.",
+)
+@click.option(
+    "-s",
+    "--study_dir",
+    required=True,
+    help="Input directory to where all the individual analyses subdirectories for merging",
+    type=click.Path(exists=True, file_okay=False),
+)
+@click.option(
+    "-p",
+    "--output_prefix",
+    required=True,
+    help="Prefix for generated merged summary files",
+    type=str,
+)
+def merge_summaries(study_dir: str, output_prefix: str) -> None:
+    """
+    Merge multiple study-level summary files into combined summary files.
+
+    :param study_dir: Path to the directory containing study-level summary files.
+    :param output_prefix: Prefix for the output merged summary files.
+    """
+
+    def get_file_paths(summary_type: str) -> list[str]:
+        return glob.glob(f"{study_dir}/*_{summary_type}_{OUTPUT_SUFFIX}")
+
+    logging.info("Generating combined assembly-level summaries")
+    logging.info("Parsing summary files for taxonomic classification")
+    merge_taxonomy_summaries(
+        get_file_paths("taxonomy"), f"{output_prefix}_taxonomy_{OUTPUT_SUFFIX}"
+    )
+
+    for summary_type, config in SUMMARY_TYPES_MAP.items():
+        logging.info(f"Parsing summary files for {summary_type.capitalize()}.")
+        column_names = config["column_names"]
+        merge_functional_summaries(
+            get_file_paths(summary_type),
+            list(column_names.values()),
+            output_prefix,
+            summary_type,
+        )
+    logging.info("Merged assembly-level summaries were generated successfully.")
+    logging.info("Done.")
+
+
+def merge_taxonomy_summaries(summary_files: list[str], output_file_name: str) -> None:
+    """
+    Merge multiple taxonomy study-level summary files into a single study-level summary.
+
+    :param summary_files: List of paths to taxonomy summary files, each containing
+                        taxonomic classifications and counts for an individual analysis.
+    :param output_file_name: Output path for the merged taxonomy summary.
+
+    Example of input taxonomy summary file:
+    taxonomy	ERZ1049444	ERZ1049446
+    sk__Eukaryota;k__Metazoa;p__Chordata	2	10
+    sk__Eukaryota;k__Metazoa;p__Chordata;c__Mammalia;o__Primates	118	94
+    """
+    if not summary_files:
+        raise FileNotFoundError(
+            "The required taxonomic classification summary files are missing. Exiting."
+        )
+
+    summary_dfs = []
+    for file in summary_files:
+        df = pd.read_csv(file, sep="\t", index_col=0)
+        df = validate_dataframe(df, TaxonomyStudySummarySchema, file)
+        summary_dfs.append(df)
+    merged_df = pd.concat(summary_dfs, axis=1)
+    merged_df = merged_df.fillna(0).astype(int)
+
+    # Reorder columns: taxonomy first, then sorted assembly accessions
+    merged_df = merged_df[sorted(merged_df.columns)]
+    merged_df = merged_df.sort_index()
+
+    merged_df.to_csv(
+        output_file_name,
+        sep="\t",
+        index_label="taxonomy",
+    )
+
+
+def merge_functional_summaries(
+    summary_files: list[str],
+    merge_keys: list[str],
+    output_prefix: str,
+    label: Literal[
+        "go", "goslim", "interpro", "ko", "sanntis", "antismash", "pfam", "kegg_modules"
+    ],
+) -> None:
+    """
+    Merge multiple functional study-level summary files into a single study-level summary.
+
+    :param summary_files: List of paths to functional summary files, each containing
+                        annotation terms and counts for an individual analysis.
+    :param merge_keys: List of column names to merge on (e.g. term ID, description).
+    :param output_prefix: Prefix for the generated output file.
+    :param label: Label describing the functional annotation type
+    (expected one of ["go", "goslim", "interpro", "ko", "sanntis", "antismash", "pfam", "kegg_modules"]).
+
+    In the input files, column orders may vary, but the following columns are expected:
+    GO summary input:
+    GO	description	category	ERZ1049444	ERZ1049446
+    GO:0016020	membrane	cellular_component	30626	673
+    GO:0005524	ATP binding	molecular_function	30524	2873
+
+    Example of InterPro summary input:
+    IPR	description	ERZ1049444	ERZ1049446
+    IPR036291	NAD(P)-binding domain superfamily	16503	13450
+    IPR019734	Tetratricopeptide repeat	14694	11021
+
+    KEGG summary input:
+    GO	description	category	ERZ1049440	ERZ1049443
+    GO:0003677	DNA binding	molecular_function	6125	16417
+    GO:0055085	transmembrane transport	biological_process	144	13926
+
+    Sanntis summary input:
+    nearest_mibig	nearest_mibig_class	description	ERZ1049440	ERZ1049443
+    BGC0001356	RiPP	Ribosomally synthesised and Post-translationally modified Peptide	230	185
+    BGC0001432	NRP Polyketide	Nonribosomal Peptide Polyketide	0	8
+
+    Antismash summary input:
+    label	description	ERZ1049440	ERZ1049443
+    NRPS	Non-ribosomal peptide synthetase	368	0
+    arylpolyene	Aryl polyene	149	447
+
+    PFAM summary input:
+    PFAM	description	ERZ1049440	ERZ1049443
+    PF24718	HTH-like domain	468	1
+    PF06039	Malate:quinone oxidoreductase (Mqo)	490	21
+
+    KEGG modules summary input:
+    module_accession	pathway_name	pathway_class	ERZ1049440	ERZ1049443
+    M00109	C21-Steroid hormone biosynthesis, progesterone => cortisol/cortisone	Pathway modules; Lipid metabolism; Sterol biosynthesis	38.9	0.0
+    M00153	Cytochrome bd ubiquinol oxidase	Pathway modules; Energy metabolism; ATP synthesis	44.7	84.4
+    """
+    output_file_name = f"{output_prefix}_{label}_{OUTPUT_SUFFIX}"
+
+    if not summary_files:
+        logging.warning(
+            f"Skipping creation of {output_file_name} because no summaries were found for this type of functional annotation."
+        )
+        return
+
+    validation_schema = SUMMARY_TYPES_MAP[label]["study_schema"]
+
+    dfs = []
+    for filepath in summary_files:
+        df = pd.read_csv(filepath, sep="\t")
+        df = validate_dataframe(df, validation_schema, filepath)
+        dfs.append(df)
+
+    if len(dfs) == 1:
+        merged_df = dfs[0]
+    else:
+        merged_df = reduce(
+            lambda left, right: pd.merge(left, right, on=merge_keys, how="outer"), dfs
+        )
+
+    # Identify non-key columns (i.e. counts)
+    value_columns = [col for col in merged_df.columns if col not in merge_keys]
+
+    # Fill NaNs and set dtype accordingly
+    fill_value = 0.0 if label == "kegg_modules" else 0
+    dtype = float if label == "kegg_modules" else int
+    merged_df[value_columns] = merged_df[value_columns].fillna(fill_value).astype(dtype)
+
+    # Reorder columns
+    merged_df = merged_df[merge_keys + sorted(value_columns)]
+
+    merged_df.to_csv(output_file_name, sep="\t", index=False)
+
+
+if __name__ == "__main__":
+    cli()

{mgnify_pipelines_toolkit-1.0.9 → mgnify_pipelines_toolkit-1.1.1}/mgnify_pipelines_toolkit/analysis/assembly/summarise_antismash_bgcs.py

@@ -155,7 +155,7 @@ def parse_args():
     description = (
         "antiSMASH output summary generator. "
         "Script takes regions from GFF and counts its appearance in annotation. "
-        "Output columns contain classID, descriptions and count. "
+        "Output columns contain label, descriptions and count. "
         f"Descriptions were taken from pre-parsed glossary provided on antiSMASH website. "
         f"Current script supports antiSMASH results for version {ANTISMASH_VERSION} and older."
     )
@@ -202,15 +202,15 @@ def main():
         df = pd.DataFrame(dict_list)
         df = df[df["product"].notna()]
         df_grouped = (
-            df.groupby(["product"]).size().reset_index(name="Count")
-        ).sort_values(by="Count", ascending=False)
+            df.groupby(["product"]).size().reset_index(name="count")
+        ).sort_values(by="count", ascending=False)
 
         df_grouped = df_grouped.rename(
             columns={
                 "product": "label",
             }
         )
-        df_grouped["Description"] = df_grouped["label"].apply(
+        df_grouped["description"] = df_grouped["label"].apply(
             lambda x: ",".join(
                 [
                     DESCRIPTIONS.get(cls.strip().lower(), cls.strip())
@@ -218,11 +218,7 @@ def main():
                 ]
             )
         )
-        df_grouped = df_grouped[["label", "Description", "Count"]]
-        df_grouped = df_grouped.rename(columns={
-            "Description": "description",
-            "Count": "count"
-        })
+        df_grouped = df_grouped[["label", "description", "count"]]
         df_grouped.to_csv(output_filename, sep="\t", index=False)