ORForise 1.6.2__py3-none-any.whl

ORForise/Annotation_Compare.py

@@ -0,0 +1,317 @@
+from importlib import import_module
+import argparse
+import sys, os
+import gzip, csv
+import logging
+from datetime import datetime
+
+
+try:
+    from .Comparator import tool_comparison
+    from .utils import *
+except (ImportError, ModuleNotFoundError):
+    from Comparator import tool_comparison
+    from utils import *
+
+
+##########################
+
+# Consolidate printing and logging into a single block
+def _pct(n, total):
+    try:
+        return format(100 * n / total, '.2f') + '%'
+    except Exception:
+        return 'N/A'
+
+##########################
+
+def comparator(options):
+
+
+    try:
+        try:  # Detect whether fasta/gff files are .gz or text and read accordingly
+            fasta_in = gzip.open(options.genome_dna, 'rt')
+            dna_regions = fasta_load(fasta_in)
+        except:
+            fasta_in = open(options.genome_dna, 'r', encoding='unicode_escape')
+            dna_regions = fasta_load(fasta_in)
+        try:
+            gff_in = gzip.open(options.reference_annotation, 'rt')
+            dna_regions = gff_load(options, gff_in, dna_regions)
+        except:
+            gff_in = open(options.reference_annotation, 'r', encoding='unicode_escape')
+            dna_regions = gff_load(options, gff_in, dna_regions)
+    except AttributeError:
+        sys.exit("Attribute Error:\nStORF'ed GFF probably already exists - Must be deleted before running (-overwrite)")
+    except FileNotFoundError:
+        split_path = options.gff.split(os.sep)
+        sys.exit("Directory '" + split_path[-2] + "' missing fna/gff files")
+        ###############################################
+    total_ref_genes = sum(
+        len(v[2]) if isinstance(v[2], (list, tuple, set, dict, str)) else 1 for v in dna_regions.values())
+
+    #############################################
+    try:
+        tool_ = import_module('Tools.' + options.tool + '.' + options.tool, package='my_current_pkg')
+    except ModuleNotFoundError:
+        try:
+            tool_ = import_module('ORForise.Tools.' + options.tool + '.' + options.tool, package='my_current_pkg')
+        except ModuleNotFoundError:
+            sys.exit("Tool not available - Did you get the name right?")
+    tool_ = getattr(tool_, options.tool)
+    all_orfs = tool_(options.tool_prediction, dna_regions)
+    results = tool_comparison(all_orfs, dna_regions, options.verbose)
+    ############## Printing to std-out and optional csv file
+    # Ensure the output directory exists
+    os.makedirs(options.outdir, exist_ok=True)
+    # Use outname as a directory, basename for files is output-outname
+    base_out = os.path.join(options.outdir, f"{os.path.basename(options.outname)}")
+
+    # Prepare to collect summary stats for all contigs
+    contig_summaries = []
+
+    if options.outdir:
+        # Ensure the output directory exists
+        os.makedirs(options.outdir, exist_ok=True)
+        # Use outname as a directory, basename for files is output-outname
+        base_out = os.path.join(options.outdir, f"{os.path.basename(options.outname)}")
+        with open(f"{base_out}_summary.txt", 'w', encoding='utf-8') as out_file:
+            out_file.write('Genome Used: ' + str(options.genome_dna.split('/')[-1]) + '\n')
+            if options.reference_tool:
+                out_file.write('Reference Tool Used: ' + str(options.reference_tool) + '\n')
+            else:
+                out_file.write('Reference Used: ' + str(options.reference_annotation.split('/')[-1]) + '\n')
+            out_file.write('Tool Compared: ' + str(options.tool) + '\n')
+            out_file.write('Total Number of Reference Genes: ' + str(total_ref_genes) + '\n')
+            out_file.write('Number of Contigs: ' + str(len(dna_regions)) + '\n')
+            out_file.write(
+                'Contig\tGenes\tORFs\tPerfect_Matches\tPartial_Matches\tMissed_Genes\tUnmatched_ORFs\tMulti_Matched_ORFs\n')
+
+    for dna_region, result in results.items():
+        if result:
+            num_current_genes = len(dna_regions[dna_region][2])
+            num_orfs = result['pred_metrics']['Number_of_ORFs']
+            num_perfect = result['pred_metrics']['Number_of_Perfect_Matches']
+            num_partial = len(result['pred_metrics']['partial_Hits'])
+            num_missed = len(result['rep_metrics']['genes_Undetected'])
+            num_unmatched = len(result['pred_metrics']['unmatched_ORFs'])
+            num_multi = len(result['pred_metrics']['multi_Matched_ORFs'])
+            # Collect summary for this contig
+            contig_summaries.append([dna_region, num_current_genes, num_orfs, num_perfect, num_partial, num_missed, num_unmatched, num_multi])
+            num_current_genes = len(dna_regions[dna_region][2])
+            genome_name = options.reference_annotation.split('/')[-1].split('.')[0]
+            rep_metric_description, rep_metrics = get_rep_metrics(result)
+            all_metric_description, all_metrics = get_all_metrics(result)
+
+             # Safely extract metric values
+            num_orfs = result.get('pred_metrics', {}).get('Number_of_ORFs') if isinstance(result, dict) else 'N/A'
+            perfect = result.get('pred_metrics', {}).get('Number_of_Perfect_Matches') if isinstance(result, dict) else 0
+            partial = len(result.get('pred_metrics', {}).get('partial_Hits', [])) if isinstance(result, dict) else 'N/A'
+            missed = len(result.get('rep_metrics', {}).get('genes_Undetected', [])) if isinstance(result, dict) else 'N/A'
+            unmatched = len(result.get('pred_metrics', {}).get('unmatched_ORFs', [])) if isinstance(result, dict) else 'N/A'
+            multi = len(result.get('pred_metrics', {}).get('multi_Matched_ORFs', [])) if isinstance(result, dict) else 'N/A'
+
+            lines = [
+                f"These are the results for: {dna_region}",
+                f"Current Contig: {dna_region}",
+                f"Number of Genes: {num_current_genes}",
+                f"Number of ORFs: {num_orfs}",
+                f"Perfect Matches: {perfect} [{num_current_genes}] - {_pct(perfect, num_current_genes) if isinstance(num_current_genes, (int, float)) else 'N/A'}",
+                f"Partial Matches: {partial} [{num_current_genes}] - {_pct(partial, num_current_genes) if isinstance(num_current_genes, (int, float)) else 'N/A'}",
+                f"Missed Genes: {missed} [{num_current_genes}] - {_pct(missed, num_current_genes) if isinstance(num_current_genes, (int, float)) else 'N/A'}",
+                f"Unmatched ORFs: {unmatched} [{num_current_genes}] - {_pct(unmatched, num_current_genes) if isinstance(num_current_genes, (int, float)) else 'N/A'}",
+                f"Multi-matched ORFs: {multi} [{num_current_genes}] - {_pct(multi, num_current_genes) if isinstance(num_current_genes, (int, float)) else 'N/A'}"
+            ]
+
+            full_msg = '\n'.join(lines) + '\n'
+            if options.verbose:
+                print(full_msg)
+            options.output_logger.info(full_msg)
+
+            # Prepare output directory and file names for each contig
+            contig_save = dna_region.replace('/', '_').replace('\\', '_')
+            contig_dir = os.path.join(options.outdir, contig_save)
+            os.makedirs(contig_dir, exist_ok=True)
+            summary_file = os.path.join(contig_dir, "summary.txt")
+            csv_file = os.path.join(contig_dir, "metrics.csv")
+            perfect_fasta = os.path.join(contig_dir, "perfect_matches.fasta")
+            partial_fasta = os.path.join(contig_dir, "partial_matches.fasta")
+            missed_fasta = os.path.join(contig_dir, "missed_genes.fasta")
+            unmatched_fasta = os.path.join(contig_dir, "unmatched_orfs.fasta")
+            multi_fasta = os.path.join(contig_dir, "multi_matched_orfs.fasta")
+
+            # Write summary to text file
+            with open(summary_file, 'w', encoding='utf-8') as sf:
+                sf.write('Current Contig: ' + str(dna_region) + '\n')
+                sf.write('Number of Genes: ' + str(num_current_genes) + '\n')
+                sf.write('Number of ORFs: ' + str(result['pred_metrics']['Number_of_ORFs']) + '\n')
+                sf.write('Perfect Matches: ' + str(result['pred_metrics']['Number_of_Perfect_Matches']) + ' [' + str(
+                    num_current_genes) + '] - ' + format(
+                    100 * result['pred_metrics']['Number_of_Perfect_Matches'] / num_current_genes, '.2f') + '%\n')
+                sf.write('Partial Matches: ' + str(len(result['pred_metrics']['partial_Hits'])) + ' [' + str(
+                    num_current_genes) + '] - ' + format(
+                    100 * len(result['pred_metrics']['partial_Hits']) / num_current_genes, '.2f') + '%\n')
+                sf.write('Missed Genes: ' + str(len(result['rep_metrics']['genes_Undetected'])) + ' [' + str(
+                    num_current_genes) + '] - ' + format(
+                    100 * len(result['rep_metrics']['genes_Undetected']) / num_current_genes, '.2f') + '%\n')
+                sf.write('Unmatched ORFs: ' + str(len(result['pred_metrics']['unmatched_ORFs'])) + ' [' + str(
+                    num_current_genes) + '] - ' + format(
+                    100 * len(result['pred_metrics']['unmatched_ORFs']) / num_current_genes, '.2f') + '%\n')
+                sf.write('Multi-matched ORFs: ' + str(len(result['pred_metrics']['multi_Matched_ORFs'])) + ' [' + str(
+                    num_current_genes) + '] - ' + format(
+                    100 * len(result['pred_metrics']['multi_Matched_ORFs']) / num_current_genes, '.2f') + '%\n')
+
+
+            # Write metrics to CSV
+                tool_out = csv.writer(out_file, quoting=csv.QUOTE_NONE, escapechar=" ")
+                tool_out = csv.writer(out_file, quoting=csv.QUOTE_NONE, escapechar=" ")  # type: ignore[arg-type]
+                tool_out.writerow(['Representative_Metrics:'])
+                tool_out.writerow(rep_metric_description.split(','))
+                tool_out.writerow([*rep_metrics])
+                tool_out.writerow(['Prediction_Metrics:'])
+                tool_out.writerow(all_metric_description.split(','))
+                tool_out.writerow([*all_metrics])
+                tool_out.writerow(['Reference_CDS_Gene_Coverage_of_Genome'])
+                tool_out.writerow([''.join(map(str, result['rep_metrics']['gene_Coverage_Genome']))])
+                tool_out.writerow(['Predicted_CDS_Coverage_of_Genome'])
+                tool_out.writerow([''.join(map(str, result['pred_metrics']['orf_Coverage_Genome']))])
+                tool_out.writerow(['Matched_Predicted_CDS_Coverage_of_Genome'])
+                tool_out.writerow([''.join(map(str, result['pred_metrics']['matched_ORF_Coverage_Genome']))])
+
+            # Write perfect matches to FASTA
+            with open(perfect_fasta, 'w', encoding='utf-8') as f:
+                for key, value in result['pred_metrics'].get('perfect_Matches', {}).items():
+                    key_parts = key.split(',')
+                    id = f">{genome_name}_{key_parts[0]}_{key_parts[1]}_{key_parts[2]}_{key_parts[5]}"
+                    f.write(f"{id}\n{value}\n")
+
+            # Write partial matches to FASTA
+            with open(partial_fasta, 'w', encoding='utf-8') as f:
+                for key, value in result['pred_metrics'].get('partial_Hits', {}).items():
+                    key_parts = key.split(';')
+                    gene_Seq = value[0]
+                    orf_Seq = value[1]
+                    f.write(f">{key_parts[0]}_gene\n{gene_Seq}\n>{key_parts[1]}_orf\n{orf_Seq}\n")
+
+            # Write missed genes to FASTA
+            with open(missed_fasta, 'w', encoding='utf-8') as f:
+                for key, value in result['rep_metrics'].get('genes_Undetected', {}).items():
+                    key_parts = key.split(',')
+                    id = f">{genome_name}_{key_parts[0]}_{key_parts[1]}_{key_parts[2]}"
+                    f.write(f"{id}\n{value}\n")
+
+            # Write unmatched ORFs to FASTA
+            with open(unmatched_fasta, 'w', encoding='utf-8') as f:
+                for key, value in result['pred_metrics'].get('unmatched_ORFs', {}).items():
+                    key_parts = key.split(',')
+                    id = f">{options.tool}_{key_parts[0]}_{key_parts[1]}_{key_parts[2]}"
+                    f.write(f"{id}\n{value}\n")
+
+            # Write multi-matched ORFs to FASTA
+            with open(multi_fasta, 'w', encoding='utf-8') as f:
+                for key, value in result['pred_metrics'].get('multi_Matched_ORFs', {}).items():
+                    key_parts = key.split(',')
+                    multi = f">Predicted_CDS:{key_parts[0]}-{key_parts[1]}_Genes:{'|'.join(value)}"
+                    f.write(f"{multi}\n")
+        else:
+            if options.verbose:
+                print(f"No results to process for dna region - " + str(dna_region))
+            options.output_logger.info(f"No results to process for dna region - " + str(dna_region))
+
+
+    # After all contigs, append the summary table to the main summary file
+    if options.outdir and contig_summaries:
+        with open(f"{base_out}_summary.txt", 'a', encoding='utf-8') as out_file:
+            for row in contig_summaries:
+                out_file.write('\t'.join(map(str, row)) + '\n')
+            # Optionally, add overall totals
+            total_genes = sum(row[1] for row in contig_summaries)
+            total_orfs = sum(row[2] for row in contig_summaries)
+            total_perfect = sum(row[3] for row in contig_summaries)
+            total_partial = sum(row[4] for row in contig_summaries)
+            total_missed = sum(row[5] for row in contig_summaries)
+            total_unmatched = sum(row[6] for row in contig_summaries)
+            total_multi = sum(row[7] for row in contig_summaries)
+            out_file.write('\nOverall Summary:\n')
+            out_file.write(f'Number of Genes: {total_genes}\n')
+            out_file.write(f'Number of ORFs: {total_orfs}\n')
+            out_file.write(f'Perfect Matches: {total_perfect} [{total_genes}] - {100 * total_perfect / total_genes:.2f}%\n')
+            out_file.write(f'Partial Matches: {total_partial} [{total_genes}] - {100 * total_partial / total_genes:.2f}%\n')
+            out_file.write(f'Missed Genes: {total_missed} [{total_genes}] - {100 * total_missed / total_genes:.2f}%\n')
+            out_file.write(f'Unmatched ORFs: {total_unmatched} [{total_genes}] - {100 * total_unmatched / total_genes:.2f}%\n')
+            out_file.write(f'Multi-matched ORFs: {total_multi} [{total_genes}] - {100 * total_multi / total_genes:.2f}%\n')
+
+            lines = [
+                f"Combined metrics for all contigs:",
+                f"Number of Genes: {total_genes}",
+                f"Number of ORFs: {total_orfs}",
+                f"Perfect Matches: {total_perfect} [{total_genes}] - {100 * total_perfect / total_genes:.2f}%",
+                f"Partial Matches: {total_partial} [{total_genes}] - {100 * total_partial / total_genes:.2f}%",
+                f"Missed Genes: {total_missed} [{total_genes}] - {100 * total_missed / total_genes:.2f}%",
+                f"Unmatched ORFs: {total_unmatched} [{total_genes}] - {100 * total_unmatched / total_genes:.2f}%",
+                f"Multi-matched ORFs: {total_multi} [{total_genes}] - {100 * total_multi / total_genes:.2f}%"
+            ]
+
+            full_msg = '\n'.join(lines) + '\n'
+            if options.verbose:
+                print(full_msg)
+            options.output_logger.info(full_msg)
+
+
+def main():
+    print(WELCOME)
+
+    parser = argparse.ArgumentParser(description='ORForise ' + ORForise_Version + ': Annotatione-Compare Run Parameters.')
+    parser._action_groups.pop()
+
+    required = parser.add_argument_group('Required Arguments')
+    required.add_argument('-dna', dest='genome_dna', required=True, help='Genome DNA file (.fa) which both annotations '
+                                                                    'are based on')
+    required.add_argument('-ref', dest='reference_annotation', required=True,
+                        help='Which reference annotation file to use as reference?')
+    required.add_argument('-t', dest='tool', required=True, help='Which tool to analyse?')
+    required.add_argument('-tp', dest='tool_prediction', required=True,
+                        help='Tool genome prediction file (.gff) - Different Tool Parameters'
+                             ' are compared individually via separate files')
+
+    optional = parser.add_argument_group('Optional Arguments')
+    optional.add_argument('-gene_ident', action='store', dest='gene_ident', default='CDS',
+                          help='What features to consider as genes? - Default: CDS - '
+                               'Provide comma separated list of features to consider as genes (e.g. CDS,exon)')
+    optional.add_argument('-rt', dest='reference_tool', required=False,
+                          help='What type of Annotation to compare to? -- Leave blank for Ensembl reference'
+                               '- Provide tool name to compare output from two tools')
+
+    output = parser.add_argument_group('Output')
+    output.add_argument('-o', dest='outdir', required=True,
+                        help='Define directory where detailed output should be places')
+    output.add_argument('-n', dest='outname', required=False,
+                        help='Define output filename(s) prefix - If not provided, filename of reference '
+                             'annotation file will be used- <outname>_<contig_id>_ORF_Comparison.csv')
+
+    misc = parser.add_argument_group('Misc')
+    misc.add_argument('-v', dest='verbose', default='False', type=eval, choices=[True, False],
+                      help='Default - False: Print out runtime status')
+    options = parser.parse_args()
+
+    options.outname = options.outname if options.outname else options.reference_annotation.split('/')[-1].split('.')[0]
+
+    # Initialise loggers once and store on options
+    if not getattr(options, 'logger_initialized', False):
+        os.makedirs(options.outdir, exist_ok=True)
+        output_log = os.path.join(options.outdir, f"ORForise_{options.outname}_{datetime.now().strftime('%Y%m%d_%H%M%S')}.log")
+        logger = logging.getLogger('ORForise.output')
+        logger.setLevel(logging.INFO)
+        fh_out = logging.FileHandler(output_log, encoding='utf-8')
+        fh_out.setFormatter(logging.Formatter('%(message)s'))
+        logger.addHandler(fh_out)
+
+        options.output_logger = logger
+        options.logger_initialized = True
+
+
+    comparator(options)
+
+if __name__ == "__main__":
+    main()
+    print("Complete")