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Merge pull request #73 from peterk87/add-vadr
Add VADR Influenza sequence annotation
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@@ -15,5 +15,5 @@ | |
| "name": "Lung, Oliver" | ||
| } | ||
| ], | ||
| "license": "MIT", | ||
| "license": "MIT" | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,146 @@ | ||
| #!/usr/bin/env python | ||
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| import logging | ||
| import os | ||
| import re | ||
| from pathlib import Path | ||
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| import typer | ||
| from Bio import SeqIO | ||
| from Bio.SeqIO.InsdcIO import _insdc_location_string | ||
| from Bio.SeqRecord import SeqRecord | ||
| from gfflu.io import get_translation, write_gff | ||
| from rich.logging import RichHandler | ||
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| REGEX_SUBNAME = re.compile(r"(SEQUENCE-\d+)") | ||
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| def init_logging(): | ||
| from rich.traceback import install | ||
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| install(show_locals=True, width=120, word_wrap=True) | ||
| logging.basicConfig( | ||
| format="%(message)s", | ||
| datefmt="[%Y-%m-%d %X]", | ||
| level=logging.DEBUG, | ||
| handlers=[RichHandler(rich_tracebacks=True, tracebacks_show_locals=True)], | ||
| ) | ||
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| def get_namesub(namesub_txt: Path) -> dict[str, str]: | ||
| namesub = {} | ||
| with open(namesub_txt) as fh: | ||
| for line in fh: | ||
| line = line.strip() | ||
| if line == "": | ||
| continue | ||
| sub_name, original_name = line.split("\t", maxsplit=1) | ||
| namesub[sub_name] = original_name | ||
| return namesub | ||
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| def write_aa_fasta(recs: list[SeqRecord], out_file: os.PathLike) -> None: | ||
| """Write out FASTA file with amino acid sequences""" | ||
| with open(out_file, "w") as out_handle: | ||
| for rec in recs: | ||
| for feature in rec.features: | ||
| if feature.type not in {"CDS", "mat_peptide", "sig_peptide"}: | ||
| continue | ||
| try: | ||
| translation = feature.qualifiers["translation"][0] | ||
| except (KeyError, IndexError): | ||
| logging.warning( | ||
| f"Could not retrieve translation qualifier for feature {feature} from {rec}. " | ||
| "Trying to obtain translation from nucleotide sequence." | ||
| ) | ||
| translation = get_translation(rec.seq, feature.location) | ||
| try: | ||
| gene = feature.qualifiers["gene"][0] | ||
| except KeyError: | ||
| gene = "" | ||
| try: | ||
| product = feature.qualifiers["product"][0] | ||
| except KeyError: | ||
| product = "" | ||
| location_str = _insdc_location_string( | ||
| location=feature.location, rec_length=len(rec.seq) | ||
| ) | ||
| out_handle.write( | ||
| f">{rec.id}|{feature.type}|{gene}|{location_str} {product}\n{translation}\n" | ||
| ) | ||
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| def write_cds_nt_fasta(recs: list[SeqRecord], out_file: os.PathLike) -> None: | ||
| """Write out FASTA file with CDS nt sequences""" | ||
| with open(out_file, "w") as out_handle: | ||
| for rec in recs: | ||
| for feature in rec.features: | ||
| if feature.type not in {"CDS", "mat_peptide", "sig_peptide"}: | ||
| continue | ||
| subseq = str(feature.location.extract(rec.seq)) | ||
| try: | ||
| gene = feature.qualifiers["gene"][0] | ||
| except KeyError: | ||
| gene = "" | ||
| try: | ||
| product = feature.qualifiers["product"][0] | ||
| except KeyError: | ||
| product = "" | ||
| location_str = _insdc_location_string( | ||
| location=feature.location, rec_length=len(rec.seq) | ||
| ) | ||
| out_handle.write( | ||
| f">{rec.id}|{feature.type}|{gene}|{location_str} {product}\n{subseq}\n" | ||
| ) | ||
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| def output_subbed_genbank( | ||
| gbk_path: Path, | ||
| gbk_out: Path, | ||
| namesub: dict[str, str], | ||
| ) -> None: | ||
| with open(gbk_path) as fh, open(gbk_out, "w") as fout: | ||
| for line in fh: | ||
| match = REGEX_SUBNAME.search(line) | ||
| if match: | ||
| subname = match.group(1) | ||
| original_name = namesub[subname] | ||
| line = line.replace(subname, original_name) | ||
| fout.write(line) | ||
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| def main( | ||
| table2asn_genbank: Path, | ||
| namesub_txt: Path, | ||
| outdir: Path = typer.Option(Path("./"), "--outdir", "-o"), | ||
| prefix: str = typer.Option("SAMPLE", "--prefix", "-p"), | ||
| ): | ||
| init_logging() | ||
| logging.info(f"{table2asn_genbank=}") | ||
| logging.info(f"{namesub_txt=}") | ||
| logging.info(f"{outdir=}") | ||
| logging.info(f"{prefix=}") | ||
| namesub = get_namesub(namesub_txt) | ||
| logging.info(f'Read {len(namesub)} from "{namesub_txt}"') | ||
| gbk_out = outdir / f"{prefix}.gbk" | ||
| output_subbed_genbank(table2asn_genbank, gbk_out, namesub) | ||
| logging.info(f'Wrote Genbank with original names to "{gbk_out}"') | ||
| recs = list(SeqIO.parse(gbk_out, "genbank")) | ||
| logging.info( | ||
| f"Read {len(recs)} sequence records from '{gbk_out}'. Writing GFF, amino acid and nucleotide FASTAs for " | ||
| "sequence features (CDS, mature peptides, signal peptides)..." | ||
| ) | ||
| gff_out = outdir / f"{prefix}.gff" | ||
| write_gff(recs, gff_out) | ||
| logging.info(f'Wrote GFF to "{gff_out}"') | ||
| faa_out = outdir / f"{prefix}.faa" | ||
| write_aa_fasta(recs, faa_out) | ||
| logging.info(f'Wrote amino acid FASTA to "{faa_out}"') | ||
| ffn_out = outdir / f"{prefix}.ffn" | ||
| write_cds_nt_fasta(recs, ffn_out) | ||
| logging.info(f'Wrote nucleotide FASTA of gene features to "{faa_out}"') | ||
| logging.info("Done!") | ||
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| if __name__ == "__main__": | ||
| typer.run(main) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,70 @@ | ||
| #!/usr/bin/env python | ||
|
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||
| import logging | ||
| from pathlib import Path | ||
|
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| import typer | ||
| from rich.logging import RichHandler | ||
|
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|
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| def init_logging(): | ||
| from rich.traceback import install | ||
|
|
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| install(show_locals=True, width=120, word_wrap=True) | ||
| logging.basicConfig( | ||
| format="%(message)s", | ||
| datefmt="[%Y-%m-%d %X]", | ||
| level=logging.DEBUG, | ||
| handlers=[RichHandler(rich_tracebacks=True, tracebacks_show_locals=True)], | ||
| ) | ||
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| def main( | ||
| input_fasta: Path = typer.Option(..., "--input-fasta", "-f"), | ||
| input_feature_table: Path = typer.Option(..., "--input-feature-table", "-t"), | ||
| outdir: Path = typer.Option(Path("./"), "--outdir", "-o"), | ||
| prefix: str = typer.Option("SAMPLE", "--prefix", "-p"), | ||
| ): | ||
| init_logging() | ||
| logging.info(f"{input_fasta=}") | ||
| logging.info(f"{input_feature_table=}") | ||
| logging.info(f"{outdir=}") | ||
| logging.info(f"{prefix=}") | ||
| ft_seqids = [] | ||
| ft_out = outdir / f"{prefix}.tbl" | ||
| with input_feature_table.open() as fh, ft_out.open("w") as fout: | ||
| seqid_count = 0 | ||
| for line in fh: | ||
| if line.startswith(">Feature "): | ||
| seqid = line.replace(">Feature ", "").strip() | ||
| seqid_count += 1 | ||
| new_seqid = f"SEQUENCE-{seqid_count}" | ||
| ft_seqids.append((seqid, new_seqid)) | ||
| fout.write(line.replace(seqid, new_seqid)) | ||
| logging.info(f"table2asn compatible feature table written to '{ft_out}'") | ||
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| namesub_path = outdir / f"{prefix}.namesub.txt" | ||
| with namesub_path.open("w") as fout: | ||
| for seqid, new_seqid in ft_seqids: | ||
| fout.write(f"{new_seqid}\t{seqid}\n") | ||
| logging.info( | ||
| f"Text file with original and table2asn seqids written to '{namesub_path}'", | ||
| ) | ||
| fasta_out = outdir / f"{prefix}.fa" | ||
| seqid_to_new_seqid = dict(ft_seqids) | ||
| logging.info(f"{seqid_to_new_seqid=}") | ||
| with input_fasta.open() as fh, fasta_out.open("w") as fout: | ||
| for line in fh: | ||
| if line.startswith(">"): | ||
| seqid, *_ = line[1:].strip().split(" ") | ||
| try: | ||
| fout.write(line.replace(seqid, seqid_to_new_seqid[seqid])) | ||
| except KeyError: | ||
| logging.warning(f"{seqid=} not in feature table seqids!") | ||
| else: | ||
| fout.write(line) | ||
| logging.info(f"table2asn compatible fasta written to '{fasta_out}'") | ||
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| if __name__ == "__main__": | ||
| typer.run(main) |
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