MetaPont 0.0.2__tar.gz → 0.0.3__tar.gz

metapont-0.0.3/PKG-INFO

@@ -0,0 +1,210 @@
+Metadata-Version: 2.1
+Name: MetaPont
+Version: 0.0.3
+Summary: MetaPont - A tool to bridge the gap between the output of metagenomic tools and the analysis of the data
+Home-page: https://github.com/TheHuwsLab/MetaPont
+Author: Nicholas Dimonaco
+Author-email: nicholas@dimonaco.co.uk
+Project-URL: Bug Tracker, https://github.com/TheHuwsLab/MetaPont/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# MetaPont
+**MetaPont**  - A tool to bridge the gap between the output of metagenomic tools and the analysis of the data
+
+## Features - These are the current aims of this project  - Still under development
+
+- **Targeted Functional Analysis:** Search for specific functional IDs (e.g., GO terms) within the `_Final_Contig.tsv` files provided by the HuwsLab Metagenome Workflow (https://github.com/TheHuwsLab/Metagenome_Workflow) .
+- **Taxonomic Breakdown:** Extract genus-level taxonomy information and calculate their proportions in the dataset.
+- **Batch Processing:** Analyse all `_Final_Contig.tsv` files in a specified directory.
+- **Customisable Output:** Save results in a format suitable for downstream analysis.
+
+---
+
+## Installation
+
+### Prerequisites
+
+Ensure you have the following installed:
+
+- Python ~3.6 or later
+
+### Installation via pip
+
+MetaPont is provided as a pip distribution. 
+
+```bash
+pip install MetaPont 
+```
+
+---
+
+## Usage
+
+--- 
+### Extract-By-Function Command-line Arguments
+```Extract-By-Function -h ``` 
+```bash
+usage: Extract_By_Function.py [-h] -d DIRECTORY -f FUNCTION_ID -o OUTPUT
+                              [-m MIN_PROPORTION] [-top TOP_TAXA]
+
+MetaPont v0.0.3: Extract-By-Function - Identify taxa contributing to a
+specific function.
+
+options:
+  -h, --help            show this help message and exit
+  -d DIRECTORY, --directory DIRECTORY
+                        Directory containing TSV files to analyse.
+  -f FUNCTION_ID, --function_id FUNCTION_ID
+                        Specific function ID to search for (e.g.,
+                        'GO:0016597').
+  -o OUTPUT, --output OUTPUT
+                        Output file to save results.
+  -m MIN_PROPORTION, --min_proportion MIN_PROPORTION
+                        Minimum proportion threshold for taxa to be included
+                        in the output.
+  -top TOP_TAXA, --top_taxa TOP_TAXA
+                        Top n taxa to be included in the output.
+
+```
+
+The `Extract-By-Function` tool provides several command-line options: \
+Note: Either -m or -top is required.
+
+| Option                   | Description                                                | Required | Default |
+|--------------------------|------------------------------------------------------------|----------|---------|
+| `-d`, `--directory`      | Directory containing `_Final_Contig.tsv` files to analyse. | Yes      | None    |
+| `-f`, `--function_id`    | Functional ID to search for (e.g., `GO:0016597`).          | Yes      | None    |
+| `-m`, `--min_proportion` | Minimum proportion needed for reporting.                   | Yes/No   | None    |
+| `-top`, `--top_taxa`     | Number of taxa to report.                                  | Yes/No   | None    |
+| `-o`, `--output`         | Output file name to save results.                          | Yes      | None    |
+
+### Example
+
+To search for the functional ID `GO:0016597` in all `_Final_Contig.tsv` files within the `test_data/` directory:
+
+```bash
+Extract=By-Function -d .../test_data/Final_contig/ -f GO:0016597 -top 3 -o .../test_data/Final_Contig/Extract_By_Function_Out/results.tsv
+```
+
+---
+
+## Output
+
+The tool generates a tab-delimited output file with the following columns:
+
+1. **Sample:** Name of the processed Sample.
+2. **Taxa:** Genus-level taxonomic assignment extracted from the `Lineage` column.
+3. **Reads Assigned (Function):** Number of reads assigned to contigs with the given functional ID.
+3. **Proportion:** Proportion of reads assigned to contigs of stated Taxa with the given functional ID within the sample.
+4. **Proportion (Total Reads):** Proportion of reads assigned to contigs of stated Taxa with the given functional ID within the total reads of the sample.
+
+Example output:
+
+```
+Function ID: GO:0016597
+Sample	Taxa	Reads Assigned (Function)	Proportion (Function)	Proportion (Total Reads)
+PN0536_0001_S1_Final_Contig.tsv	Lactobacillus	111963	0.602	0.004
+PN0536_0003_S83_Final_Contig.tsv	Lactobacillus	20072	0.457	0.001
+PN0536_0002_S2_Final_Contig.tsv	Acutalibacter	145222	0.795	0.005
+PN0536_0004_S3_Final_Contig.tsv	Lactobacillus	40076	0.404	0.002
+```
+
+---
+
+
+
+### Workflow - unfinished
+
+1. The script reads `_Final_Contig.tsv` files from the specified directory.
+2. For each file, it searches for occurrences of the given functional ID within specific columns.
+3. Matches are associated with genus-level taxonomic information extracted from the `Lineage` column.
+4. Taxa proportions are calculated and saved to the output file.
+
+---
+## Extract-By-Taxa Command-line Arguments
+```Extract-By-Taxa -h ``` 
+```bash
+usage: Extract_By_Taxa.py [-h] -d DIRECTORY -t TAXON -o OUTPUT -func
+                          FUNCTIONAL_CLASSES [-top TOP_FUNCTIONS]
+
+MetaPont: Extract Top Functions by Taxon
+
+options:
+  -h, --help            show this help message and exit
+  -d DIRECTORY, --directory DIRECTORY
+                        Directory containing TSV files to analyse.
+  -t TAXON, --taxon TAXON
+                        Target taxon to search for (e.g., 'g__Bacillus').
+  -o OUTPUT, --output OUTPUT
+                        Output file to save results.
+  -func FUNCTIONAL_CLASSES, --functional_classes FUNCTIONAL_CLASSES
+                        Which functional classes to report (e.g. GO,EC,KEGG
+                        etc).
+  -top TOP_FUNCTIONS, --top_functions TOP_FUNCTIONS
+                        Top n functions to include in the output for each
+                        sample (default: 3).
+
+```
+
+The `Extract-By-Taxa` tool provides several command-line options: 
+
+
+| Option                            | Description                                                 | Required | Default |
+|-----------------------------------|-------------------------------------------------------------|----------|---------|
+| `-d`, `--directory`               | Directory containing `_Fincal_Contig.tsv` files to analyse. | Yes      | None    |
+| `-t`, `--taxon`                   | Taxa to search for (e.g., `g__Bacillus`).                   | Yes      | None    |
+| `-func`, `--functional_classes`   | Functional classes to report (e.g. GO,EC,KEGG etc).         | Yes      | None |
+| `-top`, `--top_taxa`              | Number of functions to report (default 3).                  | No       | None    |
+| `-o`, `--output`                  | Output file name to save results.                           | Yes      | None    |
+
+### Example
+
+To search for the top reported functions for taxon `g__Bacillus` in all `_Final_Contig.tsv` files within the `test_data/` directory:
+
+```bash
+Extract-By-Taxa -d .../test_data/Final_Contig -t g__Bacillus -o .../test_data/Final_Contig/Extract_By_Taxa/results.tsv  -func GO
+```
+
+---
+## Output
+
+The tool generates a tab-delimited output file with the following columns:
+
+1. **Sample:** Name of the processed Sample.
+2. **Function:** Reported 'top' function.
+3. **Num of Assignments (Functions):** Number of times the function has been assigned across all contigs reported as chosen Taxon.
+
+Example output:
+
+```
+Selected Taxon: g__Bacillus
+Sample	Function	Num of Assignments
+PN0536_0001_S1	GO:0008150	296
+PN0536_0001_S1	GO:0003674	285
+PN0536_0001_S1	GO:0005575	254
+PN0536_0003_S83	GO:0005575	45
+PN0536_0003_S83	GO:0008150	44
+PN0536_0003_S83	GO:0003674	43
+PN0536_0002_S2	GO:0005575	5
+PN0536_0002_S2	GO:0008150	5
+PN0536_0002_S2	GO:0005623	4
+PN0536_0004_S3	GO:0008150	4
+PN0536_0004_S3	GO:0003674	3
+PN0536_0004_S3	GO:0005488	3
+
+```
+
+---
+
+### Large File Handling (Might be a failure point)
+
+The script uses `csv.field_size_limit` to handle exceptionally large `.tsv` files.
+
+---
+
+

metapont-0.0.3/README.md

@@ -0,0 +1,195 @@
+# MetaPont
+**MetaPont**  - A tool to bridge the gap between the output of metagenomic tools and the analysis of the data
+
+## Features - These are the current aims of this project  - Still under development
+
+- **Targeted Functional Analysis:** Search for specific functional IDs (e.g., GO terms) within the `_Final_Contig.tsv` files provided by the HuwsLab Metagenome Workflow (https://github.com/TheHuwsLab/Metagenome_Workflow) .
+- **Taxonomic Breakdown:** Extract genus-level taxonomy information and calculate their proportions in the dataset.
+- **Batch Processing:** Analyse all `_Final_Contig.tsv` files in a specified directory.
+- **Customisable Output:** Save results in a format suitable for downstream analysis.
+
+---
+
+## Installation
+
+### Prerequisites
+
+Ensure you have the following installed:
+
+- Python ~3.6 or later
+
+### Installation via pip
+
+MetaPont is provided as a pip distribution. 
+
+```bash
+pip install MetaPont 
+```
+
+---
+
+## Usage
+
+--- 
+### Extract-By-Function Command-line Arguments
+```Extract-By-Function -h ``` 
+```bash
+usage: Extract_By_Function.py [-h] -d DIRECTORY -f FUNCTION_ID -o OUTPUT
+                              [-m MIN_PROPORTION] [-top TOP_TAXA]
+
+MetaPont v0.0.3: Extract-By-Function - Identify taxa contributing to a
+specific function.
+
+options:
+  -h, --help            show this help message and exit
+  -d DIRECTORY, --directory DIRECTORY
+                        Directory containing TSV files to analyse.
+  -f FUNCTION_ID, --function_id FUNCTION_ID
+                        Specific function ID to search for (e.g.,
+                        'GO:0016597').
+  -o OUTPUT, --output OUTPUT
+                        Output file to save results.
+  -m MIN_PROPORTION, --min_proportion MIN_PROPORTION
+                        Minimum proportion threshold for taxa to be included
+                        in the output.
+  -top TOP_TAXA, --top_taxa TOP_TAXA
+                        Top n taxa to be included in the output.
+
+```
+
+The `Extract-By-Function` tool provides several command-line options: \
+Note: Either -m or -top is required.
+
+| Option                   | Description                                                | Required | Default |
+|--------------------------|------------------------------------------------------------|----------|---------|
+| `-d`, `--directory`      | Directory containing `_Final_Contig.tsv` files to analyse. | Yes      | None    |
+| `-f`, `--function_id`    | Functional ID to search for (e.g., `GO:0016597`).          | Yes      | None    |
+| `-m`, `--min_proportion` | Minimum proportion needed for reporting.                   | Yes/No   | None    |
+| `-top`, `--top_taxa`     | Number of taxa to report.                                  | Yes/No   | None    |
+| `-o`, `--output`         | Output file name to save results.                          | Yes      | None    |
+
+### Example
+
+To search for the functional ID `GO:0016597` in all `_Final_Contig.tsv` files within the `test_data/` directory:
+
+```bash
+Extract=By-Function -d .../test_data/Final_contig/ -f GO:0016597 -top 3 -o .../test_data/Final_Contig/Extract_By_Function_Out/results.tsv
+```
+
+---
+
+## Output
+
+The tool generates a tab-delimited output file with the following columns:
+
+1. **Sample:** Name of the processed Sample.
+2. **Taxa:** Genus-level taxonomic assignment extracted from the `Lineage` column.
+3. **Reads Assigned (Function):** Number of reads assigned to contigs with the given functional ID.
+3. **Proportion:** Proportion of reads assigned to contigs of stated Taxa with the given functional ID within the sample.
+4. **Proportion (Total Reads):** Proportion of reads assigned to contigs of stated Taxa with the given functional ID within the total reads of the sample.
+
+Example output:
+
+```
+Function ID: GO:0016597
+Sample	Taxa	Reads Assigned (Function)	Proportion (Function)	Proportion (Total Reads)
+PN0536_0001_S1_Final_Contig.tsv	Lactobacillus	111963	0.602	0.004
+PN0536_0003_S83_Final_Contig.tsv	Lactobacillus	20072	0.457	0.001
+PN0536_0002_S2_Final_Contig.tsv	Acutalibacter	145222	0.795	0.005
+PN0536_0004_S3_Final_Contig.tsv	Lactobacillus	40076	0.404	0.002
+```
+
+---
+
+
+
+### Workflow - unfinished
+
+1. The script reads `_Final_Contig.tsv` files from the specified directory.
+2. For each file, it searches for occurrences of the given functional ID within specific columns.
+3. Matches are associated with genus-level taxonomic information extracted from the `Lineage` column.
+4. Taxa proportions are calculated and saved to the output file.
+
+---
+## Extract-By-Taxa Command-line Arguments
+```Extract-By-Taxa -h ``` 
+```bash
+usage: Extract_By_Taxa.py [-h] -d DIRECTORY -t TAXON -o OUTPUT -func
+                          FUNCTIONAL_CLASSES [-top TOP_FUNCTIONS]
+
+MetaPont: Extract Top Functions by Taxon
+
+options:
+  -h, --help            show this help message and exit
+  -d DIRECTORY, --directory DIRECTORY
+                        Directory containing TSV files to analyse.
+  -t TAXON, --taxon TAXON
+                        Target taxon to search for (e.g., 'g__Bacillus').
+  -o OUTPUT, --output OUTPUT
+                        Output file to save results.
+  -func FUNCTIONAL_CLASSES, --functional_classes FUNCTIONAL_CLASSES
+                        Which functional classes to report (e.g. GO,EC,KEGG
+                        etc).
+  -top TOP_FUNCTIONS, --top_functions TOP_FUNCTIONS
+                        Top n functions to include in the output for each
+                        sample (default: 3).
+
+```
+
+The `Extract-By-Taxa` tool provides several command-line options: 
+
+
+| Option                            | Description                                                 | Required | Default |
+|-----------------------------------|-------------------------------------------------------------|----------|---------|
+| `-d`, `--directory`               | Directory containing `_Fincal_Contig.tsv` files to analyse. | Yes      | None    |
+| `-t`, `--taxon`                   | Taxa to search for (e.g., `g__Bacillus`).                   | Yes      | None    |
+| `-func`, `--functional_classes`   | Functional classes to report (e.g. GO,EC,KEGG etc).         | Yes      | None |
+| `-top`, `--top_taxa`              | Number of functions to report (default 3).                  | No       | None    |
+| `-o`, `--output`                  | Output file name to save results.                           | Yes      | None    |
+
+### Example
+
+To search for the top reported functions for taxon `g__Bacillus` in all `_Final_Contig.tsv` files within the `test_data/` directory:
+
+```bash
+Extract-By-Taxa -d .../test_data/Final_Contig -t g__Bacillus -o .../test_data/Final_Contig/Extract_By_Taxa/results.tsv  -func GO
+```
+
+---
+## Output
+
+The tool generates a tab-delimited output file with the following columns:
+
+1. **Sample:** Name of the processed Sample.
+2. **Function:** Reported 'top' function.
+3. **Num of Assignments (Functions):** Number of times the function has been assigned across all contigs reported as chosen Taxon.
+
+Example output:
+
+```
+Selected Taxon: g__Bacillus
+Sample	Function	Num of Assignments
+PN0536_0001_S1	GO:0008150	296
+PN0536_0001_S1	GO:0003674	285
+PN0536_0001_S1	GO:0005575	254
+PN0536_0003_S83	GO:0005575	45
+PN0536_0003_S83	GO:0008150	44
+PN0536_0003_S83	GO:0003674	43
+PN0536_0002_S2	GO:0005575	5
+PN0536_0002_S2	GO:0008150	5
+PN0536_0002_S2	GO:0005623	4
+PN0536_0004_S3	GO:0008150	4
+PN0536_0004_S3	GO:0003674	3
+PN0536_0004_S3	GO:0005488	3
+
+```
+
+---
+
+### Large File Handling (Might be a failure point)
+
+The script uses `csv.field_size_limit` to handle exceptionally large `.tsv` files.
+
+---
+
+

{metapont-0.0.2 → metapont-0.0.3}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = MetaPont
-version = v0.0.2
+version = v0.0.3
 author = Nicholas Dimonaco
 author_email = nicholas@dimonaco.co.uk
 description = MetaPont - A tool to bridge the gap between the output of metagenomic tools and the analysis of the data
@@ -28,6 +28,7 @@ include = *
 [options.entry_points]
 console_scripts = 
 	Extract-By-Function = MetaPont.Extract_By_Function:main
+	Extract-By-Taxa = MetaPont.Extract_By_Taxa:main
 
 [egg_info]
 tag_build = 

{metapont-0.0.2 → metapont-0.0.3}/src/MetaPont/Extract_By_Function.py

@@ -62,18 +62,26 @@ def main():
     )
     parser.add_argument(
         "-f", "--function_id", required=True,
-        help="Specific function ID to search for (e.g., 'GO:0002')."
+        help="Specific function ID to search for (e.g., 'GO:0016597')."
     )
     parser.add_argument(
-        "-o", "--output", default="output_taxa_details.tsv",
-        help="Output file to save results (default: output_taxa_details.tsv)."
+        "-o", "--output", required=True,
+        help="Output file to save results."
     )
     parser.add_argument(
-        "-m", "--min_proportion", type=float, default=0.05,
-        help="Minimum proportion threshold for taxa to be included in the output (default: 0.05)."
+        "-m", "--min_proportion", type=float,
+        help="Minimum proportion threshold for taxa to be included in the output."
+    )
+    parser.add_argument(
+        "-top", "--top_taxa", type=int,
+        help="Top n taxa to be included in the output."
     )
 
     options = parser.parse_args()
+    if not options.min_proportion and not options.top_taxa:
+        sys.exit("Error: Please specify either a minimum proportion or the number of top taxa to include in the output.")
+    elif options.min_proportion and options.top_taxa:
+        sys.exit("Error: Please specify either a minimum proportion or the number of top taxa to include in the output, not both.")
     print("Running MetaPont: Extract-By-Function " + MetaPont_Version)
 
     input_path = os.path.abspath(options.directory)
@@ -94,12 +102,21 @@ def main():
         out.write("Function ID: " + options.function_id + "\n")
         out.write("Sample\tTaxa\tReads Assigned (Function)\tProportion (Function)\tProportion (Total Reads)\n")
         for sample, (taxa_reads_function, total_reads_function, total_reads_all) in all_results.items():
-            for taxa, reads_function in taxa_reads_function.items():
-                proportion_function = reads_function / total_reads_function if total_reads_function > 0 else 0
-                proportion_total = reads_function / total_reads_all if total_reads_all > 0 else 0
-
-                if proportion_function >= options.min_proportion:  # Apply minimum proportion filter
-                    out.write(f"{sample}\t{taxa}\t{reads_function}\t{proportion_function:.3f}\t{proportion_total:.3f}\n")
+            if options.min_proportion:
+                for taxa, reads_function in taxa_reads_function.items():
+                    proportion_function = reads_function / total_reads_function if total_reads_function > 0 else 0
+                    proportion_total = reads_function / total_reads_all if total_reads_all > 0 else 0
+                    if proportion_function >= options.min_proportion:  # Apply minimum proportion filter
+                        out.write(f"{sample}\t{taxa}\t{reads_function}\t{proportion_function:.3f}\t{proportion_total:.3f}\n")
+            elif options.top_taxa:
+                sorted_taxa_reads = sorted(taxa_reads_function.items(), key=lambda x: x[1], reverse=True)
+                for i, (taxa, reads_function) in enumerate(sorted_taxa_reads):
+                    if i < options.top_taxa:
+                        proportion_function = reads_function / total_reads_function if total_reads_function > 0 else 0
+                        proportion_total = reads_function / total_reads_all if total_reads_all > 0 else 0
+                        out.write(f"{sample.replace('_Final_Contig.tsv','')}\t{taxa}\t{reads_function}\t{proportion_function:.3f}\t{proportion_total:.3f}\n")
+                    else:
+                        break
 
     print(f"Results saved to {options.output}")
 

metapont-0.0.3/src/MetaPont/Extract_By_Taxa.py

@@ -0,0 +1,130 @@
+import argparse
+import os
+import csv
+import sys
+from collections import defaultdict
+
+# Adjust constants import for module vs. standalone script usage
+try:
+    from .constants import *
+except (ModuleNotFoundError, ImportError, NameError, TypeError):
+    from constants import *
+
+# Needed to account for the large CSV/TSV files
+csv.field_size_limit(sys.maxsize)
+
+
+def process_tsv_by_taxon(file_path, target_taxon):
+    """
+    Processes a TSV file to calculate the top functions grouped by taxon.
+
+    Parameters:
+        file_path (str): Path to the TSV file.
+        target_taxon (str): Taxon to search for in the lineage column.
+
+    Returns:
+        taxon_function_reads (dict): A dictionary mapping functions to their total reads for the specified taxon.
+        total_reads_taxon (int): Total reads assigned to the specified taxon across all functions.
+    """
+    taxon_function_presence = defaultdict(int)  # Reads for each function for the specified taxon
+    total_reads_taxon = 0  # Total reads for the specified taxon
+
+    with open(file_path, "r") as tsv_file:
+        reader = csv.reader(tsv_file, delimiter="\t")
+        next(reader)  # Skip the first row (sample name)
+        headers = next(reader)  # Read headers from the second row
+
+        # Locate the necessary columns
+        taxa_idx = headers.index("Lineage")
+        reads_idx = headers.index("Mapped_Reads")
+
+        # Process each row
+        for idx, row in enumerate(reader):
+            if len(row) < len(headers):
+                continue  # Skip malformed rows
+
+            lineage = row[taxa_idx]
+            reads = int(row[reads_idx])  # Get the number of reads for this row
+
+            # Check if this row matches the specified taxon
+            if target_taxon in lineage:
+                total_reads_taxon += reads  # Increment total reads for the taxon
+
+                # Loop through the function columns (row[6:] onward)
+                for col_idx, cell in enumerate(row[6:], start=6):
+                    if cell:
+                        header = headers[col_idx]
+                        if header not in taxon_function_presence:
+                            taxon_function_presence[header] = defaultdict(int)
+                        for function in cell.replace(',', '|').split('|'):
+                            taxon_function_presence[header][function] += 1
+
+    return taxon_function_presence, total_reads_taxon
+
+
+def main():
+    parser = argparse.ArgumentParser(description='MetaPont: Extract Top Functions by Taxon')
+    parser.add_argument(
+        "-d", "--directory", required=True,
+        help="Directory containing TSV files to analyse."
+    )
+    parser.add_argument(
+        "-t", "--taxon", required=True,
+        help="Target taxon to search for (e.g., 'g__Escherichia')."
+    )
+    parser.add_argument(
+        "-o", "--output", required=True,
+        help="Output file to save results."
+    )
+    parser.add_argument(
+        "-func", "--functional_classes", required=True,
+        help="Which functional classes to report (e.g. GO,EC,KEGG etc)."
+    )
+    parser.add_argument(
+        "-top", "--top_functions", type=int, default=3,
+        help="Top n functions to include in the output for each sample (default: 3)."
+    )
+
+    options = parser.parse_args()
+    print("Running MetaPont: Extract Top Functions by Taxon")
+
+    input_path = os.path.abspath(options.directory)
+    output_path = os.path.abspath(options.output)
+
+    all_results = {}
+
+    # Process each TSV file in the directory
+    for file_name in os.listdir(input_path):
+        if file_name.endswith("_Final_Contig.tsv"):
+            file_path = os.path.join(options.directory, file_name)
+            print(f"Processing file: {file_name}")
+            taxon_function_presence, total_reads_taxon = process_tsv_by_taxon(file_path, options.taxon)
+            all_results[file_name] = (taxon_function_presence, total_reads_taxon)
+
+    # Write results to output
+    with open(output_path, "w") as out:
+        out.write("Selected Taxon: " + options.taxon + "\n")
+        out.write("Sample\tFunction\tNum of Assignments\n")
+        for sample, (taxon_function_presence, total_assignments_taxon) in all_results.items():
+            for function, assignments_dict in taxon_function_presence.items():
+                if any(func_class in function for func_class in options.functional_classes.split(',')):
+                    sorted_functions = sorted(assignments_dict.items(), key=lambda x: x[1], reverse=True)
+                    for i, (sub_function, assignments) in enumerate(sorted_functions):
+                        if i < options.top_functions:
+                            #proportion_taxon = assignments / total_reads_taxon if total_reads_taxon > 0 else 0
+                            out.write(f"{sample.replace('_Final_Contig.tsv', '')}\t{sub_function}\t{assignments}\n")
+                        else:
+                            break
+        #     sorted_functions = sorted(taxon_function_presence.items(), key=lambda x: x[1], reverse=True)
+        #     for i, (function, reads) in enumerate(sorted_functions):
+        #         if i < options.top_functions:
+        #             proportion_taxon = reads / total_reads_taxon if total_reads_taxon > 0 else 0
+        #             out.write(f"{sample.replace('_Final_Contig.tsv', '')}\t{function}\t{reads}\t{proportion_taxon:.3f}\n")
+        #         else:
+        #             break
+
+    print(f"Results saved to {options.output}")
+
+
+if __name__ == "__main__":
+    main()

metapont-0.0.3/src/MetaPont/constants.py

@@ -0,0 +1,2 @@
+MetaPont_Version = 'v0.0.3'
+

metapont-0.0.3/src/MetaPont.egg-info/PKG-INFO

@@ -0,0 +1,210 @@
+Metadata-Version: 2.1
+Name: MetaPont
+Version: 0.0.3
+Summary: MetaPont - A tool to bridge the gap between the output of metagenomic tools and the analysis of the data
+Home-page: https://github.com/TheHuwsLab/MetaPont
+Author: Nicholas Dimonaco
+Author-email: nicholas@dimonaco.co.uk
+Project-URL: Bug Tracker, https://github.com/TheHuwsLab/MetaPont/issues
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# MetaPont
+**MetaPont**  - A tool to bridge the gap between the output of metagenomic tools and the analysis of the data
+
+## Features - These are the current aims of this project  - Still under development
+
+- **Targeted Functional Analysis:** Search for specific functional IDs (e.g., GO terms) within the `_Final_Contig.tsv` files provided by the HuwsLab Metagenome Workflow (https://github.com/TheHuwsLab/Metagenome_Workflow) .
+- **Taxonomic Breakdown:** Extract genus-level taxonomy information and calculate their proportions in the dataset.
+- **Batch Processing:** Analyse all `_Final_Contig.tsv` files in a specified directory.
+- **Customisable Output:** Save results in a format suitable for downstream analysis.
+
+---
+
+## Installation
+
+### Prerequisites
+
+Ensure you have the following installed:
+
+- Python ~3.6 or later
+
+### Installation via pip
+
+MetaPont is provided as a pip distribution. 
+
+```bash
+pip install MetaPont 
+```
+
+---
+
+## Usage
+
+--- 
+### Extract-By-Function Command-line Arguments
+```Extract-By-Function -h ``` 
+```bash
+usage: Extract_By_Function.py [-h] -d DIRECTORY -f FUNCTION_ID -o OUTPUT
+                              [-m MIN_PROPORTION] [-top TOP_TAXA]
+
+MetaPont v0.0.3: Extract-By-Function - Identify taxa contributing to a
+specific function.
+
+options:
+  -h, --help            show this help message and exit
+  -d DIRECTORY, --directory DIRECTORY
+                        Directory containing TSV files to analyse.
+  -f FUNCTION_ID, --function_id FUNCTION_ID
+                        Specific function ID to search for (e.g.,
+                        'GO:0016597').
+  -o OUTPUT, --output OUTPUT
+                        Output file to save results.
+  -m MIN_PROPORTION, --min_proportion MIN_PROPORTION
+                        Minimum proportion threshold for taxa to be included
+                        in the output.
+  -top TOP_TAXA, --top_taxa TOP_TAXA
+                        Top n taxa to be included in the output.
+
+```
+
+The `Extract-By-Function` tool provides several command-line options: \
+Note: Either -m or -top is required.
+
+| Option                   | Description                                                | Required | Default |
+|--------------------------|------------------------------------------------------------|----------|---------|
+| `-d`, `--directory`      | Directory containing `_Final_Contig.tsv` files to analyse. | Yes      | None    |
+| `-f`, `--function_id`    | Functional ID to search for (e.g., `GO:0016597`).          | Yes      | None    |
+| `-m`, `--min_proportion` | Minimum proportion needed for reporting.                   | Yes/No   | None    |
+| `-top`, `--top_taxa`     | Number of taxa to report.                                  | Yes/No   | None    |
+| `-o`, `--output`         | Output file name to save results.                          | Yes      | None    |
+
+### Example
+
+To search for the functional ID `GO:0016597` in all `_Final_Contig.tsv` files within the `test_data/` directory:
+
+```bash
+Extract=By-Function -d .../test_data/Final_contig/ -f GO:0016597 -top 3 -o .../test_data/Final_Contig/Extract_By_Function_Out/results.tsv
+```
+
+---
+
+## Output
+
+The tool generates a tab-delimited output file with the following columns:
+
+1. **Sample:** Name of the processed Sample.
+2. **Taxa:** Genus-level taxonomic assignment extracted from the `Lineage` column.
+3. **Reads Assigned (Function):** Number of reads assigned to contigs with the given functional ID.
+3. **Proportion:** Proportion of reads assigned to contigs of stated Taxa with the given functional ID within the sample.
+4. **Proportion (Total Reads):** Proportion of reads assigned to contigs of stated Taxa with the given functional ID within the total reads of the sample.
+
+Example output:
+
+```
+Function ID: GO:0016597
+Sample	Taxa	Reads Assigned (Function)	Proportion (Function)	Proportion (Total Reads)
+PN0536_0001_S1_Final_Contig.tsv	Lactobacillus	111963	0.602	0.004
+PN0536_0003_S83_Final_Contig.tsv	Lactobacillus	20072	0.457	0.001
+PN0536_0002_S2_Final_Contig.tsv	Acutalibacter	145222	0.795	0.005
+PN0536_0004_S3_Final_Contig.tsv	Lactobacillus	40076	0.404	0.002
+```
+
+---
+
+
+
+### Workflow - unfinished
+
+1. The script reads `_Final_Contig.tsv` files from the specified directory.
+2. For each file, it searches for occurrences of the given functional ID within specific columns.
+3. Matches are associated with genus-level taxonomic information extracted from the `Lineage` column.
+4. Taxa proportions are calculated and saved to the output file.
+
+---
+## Extract-By-Taxa Command-line Arguments
+```Extract-By-Taxa -h ``` 
+```bash
+usage: Extract_By_Taxa.py [-h] -d DIRECTORY -t TAXON -o OUTPUT -func
+                          FUNCTIONAL_CLASSES [-top TOP_FUNCTIONS]
+
+MetaPont: Extract Top Functions by Taxon
+
+options:
+  -h, --help            show this help message and exit
+  -d DIRECTORY, --directory DIRECTORY
+                        Directory containing TSV files to analyse.
+  -t TAXON, --taxon TAXON
+                        Target taxon to search for (e.g., 'g__Bacillus').
+  -o OUTPUT, --output OUTPUT
+                        Output file to save results.
+  -func FUNCTIONAL_CLASSES, --functional_classes FUNCTIONAL_CLASSES
+                        Which functional classes to report (e.g. GO,EC,KEGG
+                        etc).
+  -top TOP_FUNCTIONS, --top_functions TOP_FUNCTIONS
+                        Top n functions to include in the output for each
+                        sample (default: 3).
+
+```
+
+The `Extract-By-Taxa` tool provides several command-line options: 
+
+
+| Option                            | Description                                                 | Required | Default |
+|-----------------------------------|-------------------------------------------------------------|----------|---------|
+| `-d`, `--directory`               | Directory containing `_Fincal_Contig.tsv` files to analyse. | Yes      | None    |
+| `-t`, `--taxon`                   | Taxa to search for (e.g., `g__Bacillus`).                   | Yes      | None    |
+| `-func`, `--functional_classes`   | Functional classes to report (e.g. GO,EC,KEGG etc).         | Yes      | None |
+| `-top`, `--top_taxa`              | Number of functions to report (default 3).                  | No       | None    |
+| `-o`, `--output`                  | Output file name to save results.                           | Yes      | None    |
+
+### Example
+
+To search for the top reported functions for taxon `g__Bacillus` in all `_Final_Contig.tsv` files within the `test_data/` directory:
+
+```bash
+Extract-By-Taxa -d .../test_data/Final_Contig -t g__Bacillus -o .../test_data/Final_Contig/Extract_By_Taxa/results.tsv  -func GO
+```
+
+---
+## Output
+
+The tool generates a tab-delimited output file with the following columns:
+
+1. **Sample:** Name of the processed Sample.
+2. **Function:** Reported 'top' function.
+3. **Num of Assignments (Functions):** Number of times the function has been assigned across all contigs reported as chosen Taxon.
+
+Example output:
+
+```
+Selected Taxon: g__Bacillus
+Sample	Function	Num of Assignments
+PN0536_0001_S1	GO:0008150	296
+PN0536_0001_S1	GO:0003674	285
+PN0536_0001_S1	GO:0005575	254
+PN0536_0003_S83	GO:0005575	45
+PN0536_0003_S83	GO:0008150	44
+PN0536_0003_S83	GO:0003674	43
+PN0536_0002_S2	GO:0005575	5
+PN0536_0002_S2	GO:0008150	5
+PN0536_0002_S2	GO:0005623	4
+PN0536_0004_S3	GO:0008150	4
+PN0536_0004_S3	GO:0003674	3
+PN0536_0004_S3	GO:0005488	3
+
+```
+
+---
+
+### Large File Handling (Might be a failure point)
+
+The script uses `csv.field_size_limit` to handle exceptionally large `.tsv` files.
+
+---
+
+

{metapont-0.0.2 → metapont-0.0.3}/src/MetaPont.egg-info/SOURCES.txt

@@ -3,6 +3,7 @@ README.md
 pyproject.toml
 setup.cfg
 src/MetaPont/Extract_By_Function.py
+src/MetaPont/Extract_By_Taxa.py
 src/MetaPont/Function_By_Taxa.py
 src/MetaPont/__init__.py
 src/MetaPont/constants.py

{metapont-0.0.2 → metapont-0.0.3}/src/MetaPont.egg-info/entry_points.txt

@@ -1,2 +1,3 @@
 [console_scripts]
 Extract-By-Function = MetaPont.Extract_By_Function:main
+Extract-By-Taxa = MetaPont.Extract_By_Taxa:main

metapont-0.0.2/PKG-INFO

@@ -1,130 +0,0 @@
-Metadata-Version: 2.1
-Name: MetaPont
-Version: 0.0.2
-Summary: MetaPont - A tool to bridge the gap between the output of metagenomic tools and the analysis of the data
-Home-page: https://github.com/TheHuwsLab/MetaPont
-Author: Nicholas Dimonaco
-Author-email: nicholas@dimonaco.co.uk
-Project-URL: Bug Tracker, https://github.com/TheHuwsLab/MetaPont/issues
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-# MetaPont
-**MetaPont**  - A tool to bridge the gap between the output of metagenomic tools and the analysis of the data
-
-## Features - These are the current aims of this project  - Still under development
-
-- **Targeted Functional Analysis:** Search for specific functional IDs (e.g., GO terms) within the `.tsv` files provided by the HuwsLab Metagenome Workflow (https://github.com/TheHuwsLab/Metagenome_Workflow) .
-- **Taxonomic Breakdown:** Extract genus-level taxonomy information and calculate their proportions in the dataset.
-- **Batch Processing:** Analyse all `.tsv` files in a specified directory.
-- **Customisable Output:** Save results in a format suitable for downstream analysis.
-
----
-
-## Installation
-
-### Prerequisites
-
-Ensure you have the following installed:
-
-- Python ~3.6 or later
-- Required Python libraries: `argparse`, `csv`, and `collections` (standard libs).
-
-### Installation via pip
-
-MetaPont is provided as a pip distribution. 
-
-```bash
-pip install MetaPont 
-```
-
----
-
-## Usage
-
-### Command-line Arguments
-```Extract-By-Function -h ``` 
-```bash
-usage: Extract-By-Function [-h] -d DIRECTORY -f FUNCTION_ID [-o OUTPUT] [-m MIN_PROPORTION]
-
-MetaPont v0.0.2: Extract-By-Function - Identify taxa contributing to a specific function.
-
-options:
-  -h, --help            show this help message and exit
-  -d DIRECTORY, --directory DIRECTORY
-                        Directory containing TSV files to analyse.
-  -f FUNCTION_ID, --function_id FUNCTION_ID
-                        Specific function ID to search for (e.g., 'GO:0002').
-  -o OUTPUT, --output OUTPUT
-                        Output file to save results (default: output_taxa_details.tsv).
-  -m MIN_PROPORTION, --min_proportion MIN_PROPORTION
-                        Minimum proportion threshold for taxa to be included in the output (default: 0.05).
-```
-
-The `Extract-By-Function` tool provides several command-line options:
-
-| Option                   | Description                                   | Required | Default                       |
-|--------------------------|-----------------------------------------------|----------|-------------------------------|
-| `-d`, `--directory`      | Directory containing `.tsv` files to analyse. | Yes      | None                          |
-| `-f`, `--function_id`    | Functional ID to search for (e.g., `GO:0002`). | Yes      | None                          |
-| `-m`, `--min_proportion` | Minimum proportion needed for reporting.      | Yes      | 0.05 (5%)                     |
-| `-o`, `--output`         | Output file name to save results.             | No       | `output_taxa_proportions.tsv` |
-
-### Example
-
-To search for the functional ID `GO:0002` in all `.tsv` files within the `data/` directory:
-
-```bash
-ExtractByFunction -d .../test_data/Final_contig/ -f GO:0002 -m 0.10 -o .../test_data/Final_Contig/Extract_By_Function_Out/results.tsv
-```
-
----
-
-## Output
-
-The tool generates a tab-delimited output file with the following columns:
-
-1. **Sample:** Name of the processed `.tsv` file.
-2. **Taxa:** Genus-level taxonomic assignment extracted from the `Lineage` column.
-3. **Proportion:** Proportion of matches to the given functional ID within the sample.
-
-Example output:
-
-```
-Function ID: GO:0002
-Sample	Taxa	Reads Assigned (Function)	Proportion (Function)	Proportion (Total Reads)
-PN0536_0003_S83_Final_Contig.tsv	Gordonibacter	60788	0.075	0.002
-PN0536_0003_S83_Final_Contig.tsv	Streptomyces	115671	0.142	0.004
-PN0536_0003_S83_Final_Contig.tsv	unknown	80890	0.099	0.003
-PN0536_0003_S83_Final_Contig.tsv	Clostridium	51018	0.063	0.002
-PN0536_0003_S83_Final_Contig.tsv	Lactobacillus	149909	0.184	0.005
-PN0536_0003_S83_Final_Contig.tsv	Limosilactobacillus	79694	0.098	0.003
-```
-
----
-
-## Implementation Details
-
-### Workflow
-
-1. The script reads `.tsv` files from the specified directory.
-2. For each file, it searches for occurrences of the given functional ID within specific columns.
-3. Matches are associated with genus-level taxonomic information extracted from the `Lineage` column.
-4. Taxa proportions are calculated and saved to the output file.
-
-### Large File Handling (Might be a failure point)
-
-The script uses `csv.field_size_limit` to handle exceptionally large `.tsv` files.
-
----
-
-## Future Plans
-
-- Add support for additional file formats (e.g., `.csv`, `.txt`).
-- Expand functionality for more complex taxonomic and functional analyses.
----
-

metapont-0.0.2/README.md

@@ -1,115 +0,0 @@
-# MetaPont
-**MetaPont**  - A tool to bridge the gap between the output of metagenomic tools and the analysis of the data
-
-## Features - These are the current aims of this project  - Still under development
-
-- **Targeted Functional Analysis:** Search for specific functional IDs (e.g., GO terms) within the `.tsv` files provided by the HuwsLab Metagenome Workflow (https://github.com/TheHuwsLab/Metagenome_Workflow) .
-- **Taxonomic Breakdown:** Extract genus-level taxonomy information and calculate their proportions in the dataset.
-- **Batch Processing:** Analyse all `.tsv` files in a specified directory.
-- **Customisable Output:** Save results in a format suitable for downstream analysis.
-
----
-
-## Installation
-
-### Prerequisites
-
-Ensure you have the following installed:
-
-- Python ~3.6 or later
-- Required Python libraries: `argparse`, `csv`, and `collections` (standard libs).
-
-### Installation via pip
-
-MetaPont is provided as a pip distribution. 
-
-```bash
-pip install MetaPont 
-```
-
----
-
-## Usage
-
-### Command-line Arguments
-```Extract-By-Function -h ``` 
-```bash
-usage: Extract-By-Function [-h] -d DIRECTORY -f FUNCTION_ID [-o OUTPUT] [-m MIN_PROPORTION]
-
-MetaPont v0.0.2: Extract-By-Function - Identify taxa contributing to a specific function.
-
-options:
-  -h, --help            show this help message and exit
-  -d DIRECTORY, --directory DIRECTORY
-                        Directory containing TSV files to analyse.
-  -f FUNCTION_ID, --function_id FUNCTION_ID
-                        Specific function ID to search for (e.g., 'GO:0002').
-  -o OUTPUT, --output OUTPUT
-                        Output file to save results (default: output_taxa_details.tsv).
-  -m MIN_PROPORTION, --min_proportion MIN_PROPORTION
-                        Minimum proportion threshold for taxa to be included in the output (default: 0.05).
-```
-
-The `Extract-By-Function` tool provides several command-line options:
-
-| Option                   | Description                                   | Required | Default                       |
-|--------------------------|-----------------------------------------------|----------|-------------------------------|
-| `-d`, `--directory`      | Directory containing `.tsv` files to analyse. | Yes      | None                          |
-| `-f`, `--function_id`    | Functional ID to search for (e.g., `GO:0002`). | Yes      | None                          |
-| `-m`, `--min_proportion` | Minimum proportion needed for reporting.      | Yes      | 0.05 (5%)                     |
-| `-o`, `--output`         | Output file name to save results.             | No       | `output_taxa_proportions.tsv` |
-
-### Example
-
-To search for the functional ID `GO:0002` in all `.tsv` files within the `data/` directory:
-
-```bash
-ExtractByFunction -d .../test_data/Final_contig/ -f GO:0002 -m 0.10 -o .../test_data/Final_Contig/Extract_By_Function_Out/results.tsv
-```
-
----
-
-## Output
-
-The tool generates a tab-delimited output file with the following columns:
-
-1. **Sample:** Name of the processed `.tsv` file.
-2. **Taxa:** Genus-level taxonomic assignment extracted from the `Lineage` column.
-3. **Proportion:** Proportion of matches to the given functional ID within the sample.
-
-Example output:
-
-```
-Function ID: GO:0002
-Sample	Taxa	Reads Assigned (Function)	Proportion (Function)	Proportion (Total Reads)
-PN0536_0003_S83_Final_Contig.tsv	Gordonibacter	60788	0.075	0.002
-PN0536_0003_S83_Final_Contig.tsv	Streptomyces	115671	0.142	0.004
-PN0536_0003_S83_Final_Contig.tsv	unknown	80890	0.099	0.003
-PN0536_0003_S83_Final_Contig.tsv	Clostridium	51018	0.063	0.002
-PN0536_0003_S83_Final_Contig.tsv	Lactobacillus	149909	0.184	0.005
-PN0536_0003_S83_Final_Contig.tsv	Limosilactobacillus	79694	0.098	0.003
-```
-
----
-
-## Implementation Details
-
-### Workflow
-
-1. The script reads `.tsv` files from the specified directory.
-2. For each file, it searches for occurrences of the given functional ID within specific columns.
-3. Matches are associated with genus-level taxonomic information extracted from the `Lineage` column.
-4. Taxa proportions are calculated and saved to the output file.
-
-### Large File Handling (Might be a failure point)
-
-The script uses `csv.field_size_limit` to handle exceptionally large `.tsv` files.
-
----
-
-## Future Plans
-
-- Add support for additional file formats (e.g., `.csv`, `.txt`).
-- Expand functionality for more complex taxonomic and functional analyses.
----
-

metapont-0.0.2/src/MetaPont/constants.py

@@ -1,2 +0,0 @@
-MetaPont_Version = 'v0.0.2'
-

metapont-0.0.2/src/MetaPont.egg-info/PKG-INFO

@@ -1,130 +0,0 @@
-Metadata-Version: 2.1
-Name: MetaPont
-Version: 0.0.2
-Summary: MetaPont - A tool to bridge the gap between the output of metagenomic tools and the analysis of the data
-Home-page: https://github.com/TheHuwsLab/MetaPont
-Author: Nicholas Dimonaco
-Author-email: nicholas@dimonaco.co.uk
-Project-URL: Bug Tracker, https://github.com/TheHuwsLab/MetaPont/issues
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-# MetaPont
-**MetaPont**  - A tool to bridge the gap between the output of metagenomic tools and the analysis of the data
-
-## Features - These are the current aims of this project  - Still under development
-
-- **Targeted Functional Analysis:** Search for specific functional IDs (e.g., GO terms) within the `.tsv` files provided by the HuwsLab Metagenome Workflow (https://github.com/TheHuwsLab/Metagenome_Workflow) .
-- **Taxonomic Breakdown:** Extract genus-level taxonomy information and calculate their proportions in the dataset.
-- **Batch Processing:** Analyse all `.tsv` files in a specified directory.
-- **Customisable Output:** Save results in a format suitable for downstream analysis.
-
----
-
-## Installation
-
-### Prerequisites
-
-Ensure you have the following installed:
-
-- Python ~3.6 or later
-- Required Python libraries: `argparse`, `csv`, and `collections` (standard libs).
-
-### Installation via pip
-
-MetaPont is provided as a pip distribution. 
-
-```bash
-pip install MetaPont 
-```
-
----
-
-## Usage
-
-### Command-line Arguments
-```Extract-By-Function -h ``` 
-```bash
-usage: Extract-By-Function [-h] -d DIRECTORY -f FUNCTION_ID [-o OUTPUT] [-m MIN_PROPORTION]
-
-MetaPont v0.0.2: Extract-By-Function - Identify taxa contributing to a specific function.
-
-options:
-  -h, --help            show this help message and exit
-  -d DIRECTORY, --directory DIRECTORY
-                        Directory containing TSV files to analyse.
-  -f FUNCTION_ID, --function_id FUNCTION_ID
-                        Specific function ID to search for (e.g., 'GO:0002').
-  -o OUTPUT, --output OUTPUT
-                        Output file to save results (default: output_taxa_details.tsv).
-  -m MIN_PROPORTION, --min_proportion MIN_PROPORTION
-                        Minimum proportion threshold for taxa to be included in the output (default: 0.05).
-```
-
-The `Extract-By-Function` tool provides several command-line options:
-
-| Option                   | Description                                   | Required | Default                       |
-|--------------------------|-----------------------------------------------|----------|-------------------------------|
-| `-d`, `--directory`      | Directory containing `.tsv` files to analyse. | Yes      | None                          |
-| `-f`, `--function_id`    | Functional ID to search for (e.g., `GO:0002`). | Yes      | None                          |
-| `-m`, `--min_proportion` | Minimum proportion needed for reporting.      | Yes      | 0.05 (5%)                     |
-| `-o`, `--output`         | Output file name to save results.             | No       | `output_taxa_proportions.tsv` |
-
-### Example
-
-To search for the functional ID `GO:0002` in all `.tsv` files within the `data/` directory:
-
-```bash
-ExtractByFunction -d .../test_data/Final_contig/ -f GO:0002 -m 0.10 -o .../test_data/Final_Contig/Extract_By_Function_Out/results.tsv
-```
-
----
-
-## Output
-
-The tool generates a tab-delimited output file with the following columns:
-
-1. **Sample:** Name of the processed `.tsv` file.
-2. **Taxa:** Genus-level taxonomic assignment extracted from the `Lineage` column.
-3. **Proportion:** Proportion of matches to the given functional ID within the sample.
-
-Example output:
-
-```
-Function ID: GO:0002
-Sample	Taxa	Reads Assigned (Function)	Proportion (Function)	Proportion (Total Reads)
-PN0536_0003_S83_Final_Contig.tsv	Gordonibacter	60788	0.075	0.002
-PN0536_0003_S83_Final_Contig.tsv	Streptomyces	115671	0.142	0.004
-PN0536_0003_S83_Final_Contig.tsv	unknown	80890	0.099	0.003
-PN0536_0003_S83_Final_Contig.tsv	Clostridium	51018	0.063	0.002
-PN0536_0003_S83_Final_Contig.tsv	Lactobacillus	149909	0.184	0.005
-PN0536_0003_S83_Final_Contig.tsv	Limosilactobacillus	79694	0.098	0.003
-```
-
----
-
-## Implementation Details
-
-### Workflow
-
-1. The script reads `.tsv` files from the specified directory.
-2. For each file, it searches for occurrences of the given functional ID within specific columns.
-3. Matches are associated with genus-level taxonomic information extracted from the `Lineage` column.
-4. Taxa proportions are calculated and saved to the output file.
-
-### Large File Handling (Might be a failure point)
-
-The script uses `csv.field_size_limit` to handle exceptionally large `.tsv` files.
-
----
-
-## Future Plans
-
-- Add support for additional file formats (e.g., `.csv`, `.txt`).
-- Expand functionality for more complex taxonomic and functional analyses.
----
-