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Merge pull request #1107 from nf-core/stringtie_gtf
Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| #!/usr/bin/env python | ||
| import logging | ||
| import argparse | ||
| import re | ||
| import statistics | ||
| from typing import Set | ||
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| # Create a logger | ||
| logging.basicConfig(format="%(name)s - %(asctime)s %(levelname)s: %(message)s") | ||
| logger = logging.getLogger("fasta_gtf_filter") | ||
| logger.setLevel(logging.INFO) | ||
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| def extract_fasta_seq_names(fasta_name: str) -> Set[str]: | ||
| """Extracts the sequence names from a FASTA file.""" | ||
| with open(fasta_name) as fasta: | ||
| return {line[1:].split(None, 1)[0] for line in fasta if line.startswith(">")} | ||
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| def tab_delimited(file: str) -> float: | ||
| """Check if file is tab-delimited and return median number of tabs.""" | ||
| with open(file, "r") as f: | ||
| data = f.read(1024) | ||
| return statistics.median(line.count("\t") for line in data.split("\n")) | ||
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| def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool) -> None: | ||
| """Filter GTF file based on FASTA sequence names.""" | ||
| if tab_delimited(gtf_in) != 8: | ||
| raise ValueError("Invalid GTF file: Expected 8 tab-separated columns.") | ||
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| seq_names_in_genome = extract_fasta_seq_names(fasta) | ||
| logger.info(f"Extracted chromosome sequence names from {fasta}") | ||
| logger.debug("All sequence IDs from FASTA: " + ", ".join(sorted(seq_names_in_genome))) | ||
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| seq_names_in_gtf = set() | ||
| try: | ||
| with open(gtf_in) as gtf, open(filtered_gtf_out, "w") as out: | ||
| line_count = 0 | ||
| for line in gtf: | ||
| seq_name = line.split("\t")[0] | ||
| seq_names_in_gtf.add(seq_name) # Add sequence name to the set | ||
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| if seq_name in seq_names_in_genome: | ||
| if skip_transcript_id_check or re.search(r'transcript_id "([^"]+)"', line): | ||
| out.write(line) | ||
| line_count += 1 | ||
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| if line_count == 0: | ||
| raise ValueError("All GTF lines removed by filters") | ||
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| except IOError as e: | ||
| logger.error(f"File operation failed: {e}") | ||
| return | ||
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| logger.debug("All sequence IDs from GTF: " + ", ".join(sorted(seq_names_in_gtf))) | ||
| logger.info(f"Extracted {line_count} matching sequences from {gtf_in} into {filtered_gtf_out}") | ||
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| if __name__ == "__main__": | ||
| parser = argparse.ArgumentParser(description="Filters a GTF file based on sequence names in a FASTA file.") | ||
| parser.add_argument("--gtf", type=str, required=True, help="GTF file") | ||
| parser.add_argument("--fasta", type=str, required=True, help="Genome fasta file") | ||
| parser.add_argument("--prefix", dest="prefix", default="genes", type=str, help="Prefix for output GTF files") | ||
| parser.add_argument( | ||
| "--skip_transcript_id_check", action="store_true", help="Skip checking for transcript IDs in the GTF file" | ||
| ) | ||
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| args = parser.parse_args() | ||
| filter_gtf(args.fasta, args.gtf, args.prefix + ".filtered.gtf", args.skip_transcript_id_check) |
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