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Merge pull request #161 from sanger-tol/dev
2.1.0 release
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| #!/usr/bin/env python3 | ||
| import re | ||
| import csv | ||
| import sys | ||
| import argparse | ||
| import json | ||
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| # Extract CDS information from mrna and transcript sections | ||
| def extract_cds_info(file): | ||
| # Define regex patterns for different statistics | ||
| patterns = { | ||
| "TRANSC_MRNA": re.compile(r"Number of mrna\s+(\d+)"), | ||
| "PCG": re.compile(r"Number of gene\s+(\d+)"), | ||
| "CDS_PER_GENE": re.compile(r"mean mrnas per gene\s+([\d.]+)"), | ||
| "EXONS_PER_TRANSC": re.compile(r"mean exons per mrna\s+([\d.]+)"), | ||
| "CDS_LENGTH": re.compile(r"mean mrna length \(bp\)\s+([\d.]+)"), | ||
| "EXON_SIZE": re.compile(r"mean exon length \(bp\)\s+([\d.]+)"), | ||
| "INTRON_SIZE": re.compile(r"mean intron in cds length \(bp\)\s+([\d.]+)"), | ||
| } | ||
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| # Initialize a dictionary to store content for different sections | ||
| section_content = {"mrna": "", "transcript": ""} | ||
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| # Variable to keep track of the current section being processed | ||
| current_section = None | ||
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| with open(file, "r") as f: | ||
| lines = f.read().splitlines() # read all lines in the file | ||
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| for line in lines: | ||
| line = line.strip() # Remove any leading/trailing whitespace including newline characters | ||
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| if "---------------------------------- mrna ----------------------------------" in line: | ||
| current_section = "mrna" # Switch to 'mrna' section | ||
| elif "---------------------------------- transcript ----------------------------------" in line: | ||
| current_section = "transcript" # Switch to 'transcript' section | ||
| elif "----------" in line: | ||
| current_section = None # End of current section | ||
| elif current_section: | ||
| section_content[current_section] += ( | ||
| line + " " | ||
| ) # Accumulate content for the current section, separate lines by a space | ||
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| cds_info = {} | ||
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| for label, pattern in patterns.items(): | ||
| text_to_search = section_content["mrna"] if label != "EXONS_PER_TRANSC" else section_content["transcript"] | ||
| match = re.search(pattern, text_to_search) | ||
| if match: | ||
| cds_info[label] = match.group(1) | ||
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| return cds_info | ||
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| # Function to extract the number of non-coding genes from the second file | ||
| def extract_non_coding_genes(file): | ||
| non_coding_genes = {"ncrna_gene": 0} | ||
|
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| with open(file, "r") as f: | ||
| for line in f: | ||
| parts = line.split() | ||
| if len(parts) < 2: | ||
| continue | ||
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| gene_type = parts[0] | ||
| try: | ||
| count = int(parts[1]) | ||
| except ValueError: | ||
| continue | ||
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| if gene_type in non_coding_genes: | ||
| non_coding_genes[gene_type] += count | ||
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| NCG = sum(non_coding_genes.values()) | ||
| return {"NCG": NCG} | ||
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| # Extract the one_line_summary from a BUSCO JSON file | ||
| def extract_busco_results(busco_stats_file): | ||
| try: | ||
| with open(busco_stats_file, "r") as file: | ||
| busco_data = json.load(file) | ||
| # Extract the one_line_summary from the results section | ||
| one_line_summary = busco_data.get("results", {}).get("one_line_summary") | ||
| if one_line_summary: | ||
| # Use regex to extract everything after the first colon | ||
| match = re.search(r':\s*"(.*)"', one_line_summary) | ||
| if match: | ||
| one_line_summary = match.group(1) # Get text after the colon | ||
| return {"BUSCO_PROTEIN_SCORES": one_line_summary} if one_line_summary else {} | ||
| except (json.JSONDecodeError, FileNotFoundError) as e: | ||
| print(f"Error loading BUSCO JSON file: {e}") | ||
| return {} | ||
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| # Function to write the extracted data to a CSV file | ||
| def write_to_csv(data, output_file, busco_stats_file): | ||
| busco_results = extract_busco_results(busco_stats_file) | ||
|
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| descriptions = { | ||
| "TRANSC_MRNA": "The number of transcribed mRNAs", | ||
| "PCG": "The number of protein coding genes", | ||
| "NCG": "The number of non-coding genes", | ||
| "CDS_PER_GENE": "The average number of coding transcripts per gene", | ||
| "EXONS_PER_TRANSC": "The average number of exons per transcript", | ||
| "CDS_LENGTH": "The average length of coding sequence", | ||
| "EXON_SIZE": "The average length of a coding exon", | ||
| "INTRON_SIZE": "The average length of coding intron size", | ||
| "BUSCO_PROTEIN_SCORES": "BUSCO results summary from running BUSCO in protein mode", | ||
| } | ||
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| with open(output_file, "w", newline="") as csvfile: | ||
| writer = csv.writer(csvfile) | ||
|
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| # Write descriptions at the top of the CSV file | ||
| for key, description in descriptions.items(): | ||
| csvfile.write(f"# {key}: {description}\n") | ||
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| # Write the Variable and Value columns header | ||
| writer.writerow(["#paramName", "paramValue"]) | ||
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| # Write the data | ||
| for key, value in data.items(): | ||
| writer.writerow([key, value]) | ||
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| # Add the BUSCO results summary | ||
| for key, value in busco_results.items(): | ||
| writer.writerow([key, value]) | ||
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| # Main function to take input files and output file as arguments | ||
| def main(): | ||
| Description = "Parse contents of the agat_spstatistics, buscoproteins and agat_sqstatbasic to extract relevant annotation statistics information." | ||
| Epilog = ( | ||
| "Example usage: python extract_annotation_statistics_info.py <basic_stats> <other_stats> <busco_stats> <output>" | ||
| ) | ||
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| parser = argparse.ArgumentParser(description=Description, epilog=Epilog) | ||
| parser.add_argument("basic_stats", help="Input txt file with basic_feature_statistics.") | ||
| parser.add_argument("other_stats", help="Input txt file with other_feature_statistics.") | ||
| parser.add_argument("busco_stats", help="Input JSON file for the BUSCO statistics.") | ||
| parser.add_argument("output", help="Output file.") | ||
| parser.add_argument("--version", action="version", version="%(prog)s 1.0") | ||
| args = parser.parse_args() | ||
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| cds_info = extract_cds_info(args.other_stats) | ||
| non_coding_genes = extract_non_coding_genes(args.basic_stats) | ||
| data = {**cds_info, **non_coding_genes} | ||
| write_to_csv(data, args.output, args.busco_stats) | ||
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| if __name__ == "__main__": | ||
| sys.exit(main()) |
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