MetaPont 0.0.7__tar.gz → 0.0.8__tar.gz

{metapont-0.0.7/src/MetaPont.egg-info → metapont-0.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: MetaPont
-Version: 0.0.7
+Version: 0.0.8
 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
@@ -116,6 +116,28 @@ PN0536_0004_S3_Final_Contig.tsv	Lactobacillus	40076	0.404	0.002
 
 ---
 
+# Extract-Function-By-Taxa:
+```bash
+usage: Extract_Function_By_Taxa.py [-h] -d DIRECTORY -t TAXON -f FUNCTION -o
+                                   OUTPUT
+
+MetaPont: Extract Reads Proportions for a Specific Taxon and Function
+
+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__Escherichia').
+  -f FUNCTION, --function FUNCTION
+                        Target function to extract (e.g., 'EC:2.7.11.1').
+  -o OUTPUT, --output OUTPUT
+                        Output file to save results.
+
+```
+
+
+
 
 
 ### Workflow - unfinished

{metapont-0.0.7 → metapont-0.0.8}/README.md

@@ -101,6 +101,28 @@ PN0536_0004_S3_Final_Contig.tsv	Lactobacillus	40076	0.404	0.002
 
 ---
 
+# Extract-Function-By-Taxa:
+```bash
+usage: Extract_Function_By_Taxa.py [-h] -d DIRECTORY -t TAXON -f FUNCTION -o
+                                   OUTPUT
+
+MetaPont: Extract Reads Proportions for a Specific Taxon and Function
+
+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__Escherichia').
+  -f FUNCTION, --function FUNCTION
+                        Target function to extract (e.g., 'EC:2.7.11.1').
+  -o OUTPUT, --output OUTPUT
+                        Output file to save results.
+
+```
+
+
+
 
 
 ### Workflow - unfinished

{metapont-0.0.7 → metapont-0.0.8}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = MetaPont
-version = v0.0.7
+version = v0.0.8
 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
@@ -31,6 +31,8 @@ console_scripts =
 	extract-by-function = MetaPont.Extract_By_Function:main
 	Extract-By-Taxa = MetaPont.Extract_By_Taxa:main
 	extract-by-taxa = MetaPont.Extract_By_Taxa:main
+	Extract-Function-By-Taxa = MetaPont.Extract_Function_By_Taxa:main
+	extract-function-by-taxa = MetaPont.Extract_Function_By_Taxa:main
 	Extract-Reads-By-Function = MetaPont.Extract_Reads_By_Function:main
 	extract-reads-by-function = MetaPont.Extract_Reads_By_Function:main
 	kraken-emapper-readmap-combine = kraken_emapper_readmap_combiner:main

metapont-0.0.8/src/MetaPont/Extract_Function_By_Taxa.py

@@ -0,0 +1,130 @@
+import argparse
+import os
+import csv
+import sys
+from collections import defaultdict
+
+# Needed to account for large CSV/TSV files
+csv.field_size_limit(sys.maxsize)
+
+def process_tsv_by_taxon_and_function(file_path, target_taxon, target_function):
+    """
+    Processes a TSV file to calculate the proportion of reads assigned to a taxon and function
+    relative to all reads assigned to that function across all taxa.
+
+    Parameters:
+        file_path (str): Path to the TSV file.
+        target_taxon (str): Taxon to search for in the lineage column.
+        target_function (str): Function to search for in the function columns.
+
+    Returns:
+        function_proportion (float): Proportion of reads assigned to the function within the taxon
+                                     relative to all reads assigned to the function.
+        reads_taxon_function (int): Total reads assigned to the taxon and function.
+        total_reads_function (int): Total reads assigned to the function across all taxa.
+    """
+    reads_taxon_function = 0  # Reads assigned to the specified taxon and function
+    total_reads_function = 0  # Total reads assigned to the function across all taxa
+
+    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
+
+        # Ensure required columns exist
+        try:
+            taxa_idx = headers.index("Lineage")
+            reads_idx = headers.index("Mapped_Reads")
+        except ValueError:
+            print(f"Error: Required columns not found in {file_path}. Skipping...")
+            return 0, 0, 0
+
+        # Process each row
+        for row in 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 function ID
+            for cell in row[6:]:
+                if cell and any(target_function in part for part in cell.replace(',', '|').split('|')):
+                    if target_taxon in lineage:
+                       # lineage = lineage.split("s__")[0]  # .split("|")[0]
+                        reads_taxon_function += reads
+                        total_reads_function += reads
+                    else:
+                        total_reads_function += reads
+                    break  # Stop checking further functional columns for this row
+
+
+            # # Check if the function is present in this row
+            # function_present = any(target_function in cell for cell in row[6:] if cell)
+            #
+            # if function_present:
+            #     total_reads_function += reads  # Add to total function reads across all taxa
+            #
+            #     # If the taxon is also present, add to taxon-specific function reads
+            #     if target_taxon in lineage:
+            #         reads_taxon_function += reads
+
+    # Compute the proportion
+    function_proportion = reads_taxon_function / total_reads_function if total_reads_function > 0 else 0
+
+    return function_proportion, reads_taxon_function, total_reads_function
+
+
+def main():
+    parser = argparse.ArgumentParser(description='MetaPont: Extract Reads Proportions for a Specific Taxon and Function')
+    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(
+        "-f", "--function", required=True,
+        help="Target function to extract (e.g., 'EC:2.7.11.1')."
+    )
+    parser.add_argument(
+        "-o", "--output", required=True,
+        help="Output file to save results."
+    )
+
+    options = parser.parse_args()
+    print(f"Running extraction for Taxon: {options.taxon} and Function: {options.function}")
+
+    input_path = os.path.abspath(options.directory)
+    output_path = os.path.abspath(options.output)
+
+    # Store results
+    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}")
+
+            function_proportion, reads_taxon_function, total_reads_function = process_tsv_by_taxon_and_function(
+                file_path, options.taxon, options.function
+            )
+
+            # Store the result
+            results.append((file_name.replace("_Final_Contig.tsv", ""), function_proportion, reads_taxon_function, total_reads_function))
+
+    # Write results to output file
+    with open(output_path, "w") as out:
+        out.write(f"Taxon: {options.taxon}, Function: {options.function}\n")
+        out.write("Sample\tFunction Proportion\tReads in Taxon & Function\tTotal Reads in Function\n")
+        for sample, function_proportion, reads_taxon_function, total_reads_function in results:
+            out.write(f"{sample}\t{function_proportion:.6f}\t{reads_taxon_function}\t{total_reads_function}\n")
+
+    print(f"Results saved to {options.output}")
+
+
+if __name__ == "__main__":
+    main()

metapont-0.0.8/src/MetaPont/constants.py

@@ -0,0 +1,2 @@
+MetaPont_Version = 'v0.0.8'
+

{metapont-0.0.7 → metapont-0.0.8/src/MetaPont.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: MetaPont
-Version: 0.0.7
+Version: 0.0.8
 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
@@ -116,6 +116,28 @@ PN0536_0004_S3_Final_Contig.tsv	Lactobacillus	40076	0.404	0.002
 
 ---
 
+# Extract-Function-By-Taxa:
+```bash
+usage: Extract_Function_By_Taxa.py [-h] -d DIRECTORY -t TAXON -f FUNCTION -o
+                                   OUTPUT
+
+MetaPont: Extract Reads Proportions for a Specific Taxon and Function
+
+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__Escherichia').
+  -f FUNCTION, --function FUNCTION
+                        Target function to extract (e.g., 'EC:2.7.11.1').
+  -o OUTPUT, --output OUTPUT
+                        Output file to save results.
+
+```
+
+
+
 
 
 ### Workflow - unfinished

{metapont-0.0.7 → metapont-0.0.8}/src/MetaPont.egg-info/SOURCES.txt

@@ -4,6 +4,7 @@ pyproject.toml
 setup.cfg
 src/MetaPont/Extract_By_Function.py
 src/MetaPont/Extract_By_Taxa.py
+src/MetaPont/Extract_Function_By_Taxa.py
 src/MetaPont/Extract_Reads_By_Function.py
 src/MetaPont/Function_By_Taxa.py
 src/MetaPont/__init__.py

{metapont-0.0.7 → metapont-0.0.8}/src/MetaPont.egg-info/entry_points.txt

@@ -1,8 +1,10 @@
 [console_scripts]
 Extract-By-Function = MetaPont.Extract_By_Function:main
 Extract-By-Taxa = MetaPont.Extract_By_Taxa:main
+Extract-Function-By-Taxa = MetaPont.Extract_Function_By_Taxa:main
 Extract-Reads-By-Function = MetaPont.Extract_Reads_By_Function:main
 extract-by-function = MetaPont.Extract_By_Function:main
 extract-by-taxa = MetaPont.Extract_By_Taxa:main
+extract-function-by-taxa = MetaPont.Extract_Function_By_Taxa:main
 extract-reads-by-function = MetaPont.Extract_Reads_By_Function:main
 kraken-emapper-readmap-combine = kraken_emapper_readmap_combiner:main

metapont-0.0.7/src/MetaPont/constants.py

@@ -1,2 +0,0 @@
-MetaPont_Version = 'v0.0.7'
-