kkonganti@17: #!/usr/bin/env python3
kkonganti@17: 
kkonganti@17: # Kranti Konganti
kkonganti@17: 
kkonganti@17: import argparse
kkonganti@17: import inspect
kkonganti@17: import logging
kkonganti@17: import os
kkonganti@17: import re
kkonganti@17: import shutil
kkonganti@17: import ssl
kkonganti@17: import tempfile
kkonganti@17: from html.parser import HTMLParser
kkonganti@17: from urllib.request import urlopen
kkonganti@17: 
kkonganti@17: # Set logging.f
kkonganti@17: logging.basicConfig(
kkonganti@17:     format="\n" + "=" * 55 + "\n%(asctime)s - %(levelname)s\n" + "=" * 55 + "\n%(message)s\n",
kkonganti@17:     level=logging.DEBUG,
kkonganti@17: )
kkonganti@17: 
kkonganti@17: # Multiple inheritence for pretty printing of help text.
kkonganti@17: class MultiArgFormatClasses(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelpFormatter):
kkonganti@17:     pass
kkonganti@17: 
kkonganti@17: 
kkonganti@17: # HTMLParser override class to get PDG release and latest Cluster .tsv file
kkonganti@17: class NCBIPathogensHTMLParser(HTMLParser):
kkonganti@17:     def __init__(self, *, convert_charrefs: bool = ...) -> None:
kkonganti@17:         super().__init__(convert_charrefs=convert_charrefs)
kkonganti@17:         self.reset()
kkonganti@17:         self.href_data = list()
kkonganti@17: 
kkonganti@17:     def handle_data(self, data):
kkonganti@17:         self.href_data.append(data)
kkonganti@17: 
kkonganti@17: 
kkonganti@17: def dl_pdg(**kwargs) -> None:
kkonganti@17:     """
kkonganti@17:     Method to save the PDG metadata file and
kkonganti@17:     return the latest PDG release.
kkonganti@17:     """
kkonganti@17:     db_path, url, regex, suffix, overwrite, release = [kwargs[k] for k in kwargs.keys()]
kkonganti@17: 
kkonganti@17:     contxt = ssl.create_default_context()
kkonganti@17:     contxt.check_hostname = False
kkonganti@17:     contxt.verify_mode = ssl.CERT_NONE
kkonganti@17: 
kkonganti@17:     if (db_path or url) == None:
kkonganti@17:         logging.error("Please provide absolute UNIX path\n" + "to store the result DB flat files.")
kkonganti@17:         exit(1)
kkonganti@17: 
kkonganti@17:     if re.match(r"^PDG\d+\.\d+$", release):
kkonganti@17:         url = re.sub("latest_snps", release.strip(), url)
kkonganti@17: 
kkonganti@17:     html_parser = NCBIPathogensHTMLParser()
kkonganti@17:     logging.info(f"Finding latest NCBI PDG release at:\n{url}")
kkonganti@17: 
kkonganti@17:     with urlopen(url, context=contxt) as response:
kkonganti@17:         with tempfile.NamedTemporaryFile(delete=False) as tmp_html_file:
kkonganti@17:             shutil.copyfileobj(response, tmp_html_file)
kkonganti@17: 
kkonganti@17:     with open(tmp_html_file.name, "r") as html:
kkonganti@17:         html_parser.feed("".join(html.readlines()))
kkonganti@17: 
kkonganti@17:     pdg_filename = re.search(regex, "".join(html_parser.href_data)).group(0)
kkonganti@17:     pdg_release = pdg_filename.rstrip(suffix)
kkonganti@17:     pdg_metadata_url = "/".join([url, pdg_filename])
kkonganti@17:     pdg_release = pdg_filename.rstrip(suffix)
kkonganti@17:     dest_dir = os.path.join(db_path, pdg_release)
kkonganti@17: 
kkonganti@17:     logging.info(f"Found NCBI PDG file:\n{pdg_metadata_url}")
kkonganti@17: 
kkonganti@17:     if (
kkonganti@17:         not overwrite
kkonganti@17:         and re.match(r".+?\.metadata\.tsv$", pdg_filename)
kkonganti@17:         and os.path.exists(dest_dir)
kkonganti@17:     ):
kkonganti@17:         logging.error(f"DB path\n{dest_dir}\nalready exists. Please use -f to overwrite.")
kkonganti@17:         exit(1)
kkonganti@17:     elif overwrite and not re.match(r".+?\.reference_target\.cluster_list\.tsv$", pdg_filename):
kkonganti@17:         shutil.rmtree(dest_dir, ignore_errors=True) if os.path.exists(dest_dir) else None
kkonganti@17:         os.makedirs(dest_dir)
kkonganti@17:     elif (
kkonganti@17:         not overwrite
kkonganti@17:         and re.match(r".+?\.metadata\.tsv$", pdg_filename)
kkonganti@17:         and not os.path.exists(dest_dir)
kkonganti@17:     ):
kkonganti@17:         os.makedirs(dest_dir)
kkonganti@17: 
kkonganti@17:     tsv_at = os.path.join(dest_dir, pdg_filename)
kkonganti@17:     logging.info(f"Saving to:\n{tsv_at}")
kkonganti@17: 
kkonganti@17:     with urlopen(pdg_metadata_url, context=contxt) as response:
kkonganti@17:         with open(tsv_at, "w") as tsv:
kkonganti@17:             tsv.writelines(response.read().decode("utf-8"))
kkonganti@17: 
kkonganti@17:     html.close()
kkonganti@17:     tmp_html_file.close()
kkonganti@17:     os.unlink(tmp_html_file.name)
kkonganti@17:     tsv.close()
kkonganti@17:     response.close()
kkonganti@17: 
kkonganti@17:     return tsv_at, dest_dir
kkonganti@17: 
kkonganti@17: 
kkonganti@17: def main() -> None:
kkonganti@17:     """
kkonganti@17:     This script is part of the `bettercallsal_db` Nextflow workflow and is only
kkonganti@17:     tested on POSIX sytems.
kkonganti@17:     It:
kkonganti@17:         1. Downloads the latest NCBI Pathogens Release metadata file, which
kkonganti@17:             looks like PDGXXXXXXXXXX.2504.metadata.csv and also the SNP cluster
kkonganti@17:             information file which looks like PDGXXXXXXXXXX.2504.reference_target.cluster_list.tsv
kkonganti@17:         2. Generates a new metadata file with only required information such as
kkonganti@17:             computed_serotype, isolates GenBank or RefSeq downloadable genome FASTA
kkonganti@17:             URL.
kkonganti@17:     """
kkonganti@17: 
kkonganti@17:     prog_name = os.path.basename(inspect.stack()[0].filename)
kkonganti@17: 
kkonganti@17:     parser = argparse.ArgumentParser(
kkonganti@17:         prog=prog_name, description=main.__doc__, formatter_class=MultiArgFormatClasses
kkonganti@17:     )
kkonganti@17: 
kkonganti@17:     # required = parser.add_argument_group("required arguments")
kkonganti@17: 
kkonganti@17:     parser.add_argument(
kkonganti@17:         "-db",
kkonganti@17:         dest="db_path",
kkonganti@17:         default=os.getcwd(),
kkonganti@17:         required=False,
kkonganti@17:         help="Absolute UNIX path to a path where all results files are\nstored.",
kkonganti@17:     )
kkonganti@17:     parser.add_argument(
kkonganti@17:         "-f",
kkonganti@17:         dest="overwrite_db",
kkonganti@17:         default=False,
kkonganti@17:         required=False,
kkonganti@17:         action="store_true",
kkonganti@17:         help="Force overwrite a PDG release directory at DB path\nmentioned with -db.",
kkonganti@17:     )
kkonganti@17:     parser.add_argument(
kkonganti@17:         "-org",
kkonganti@17:         dest="organism",
kkonganti@17:         default="Salmonella",
kkonganti@17:         required=False,
kkonganti@17:         help="The organism to create the DB flat files\nfor.",
kkonganti@17:     )
kkonganti@17:     parser.add_argument(
kkonganti@17:         "-rel",
kkonganti@17:         dest="release",
kkonganti@17:         default=False,
kkonganti@17:         required=False,
kkonganti@17:         help="If you get a 404 error, try mentioning the actual release identifier.\n"
kkonganti@17:         + "Ex: For Salmonella, you can get the release identifier by going to:\n"
kkonganti@17:         + "    https://ftp.ncbi.nlm.nih.gov/pathogen/Results/Salmonella\n"
kkonganti@17:         + "Ex: If you want metadata beloginging to release PDG000000002.2507, then you\n"
kkonganti@17:         + "    would use this command-line option as:\n    -rel PDG000000002.2507",
kkonganti@17:     )
kkonganti@17: 
kkonganti@17:     args = parser.parse_args()
kkonganti@17:     db_path = args.db_path
kkonganti@17:     org = args.organism
kkonganti@17:     overwrite = args.overwrite_db
kkonganti@17:     release = args.release
kkonganti@17:     ncbi_pathogens_loc = "/".join(
kkonganti@17:         ["https://ftp.ncbi.nlm.nih.gov/pathogen/Results", org, "latest_snps"]
kkonganti@17:     )
kkonganti@17: 
kkonganti@17:     if not db_path:
kkonganti@17:         db_path = os.getcwd()
kkonganti@17: 
kkonganti@17:     # Save metadata
kkonganti@17:     file, dest_dir = dl_pdg(
kkonganti@17:         db_path=db_path,
kkonganti@17:         url="/".join([ncbi_pathogens_loc, "Metadata"]),
kkonganti@17:         regex=re.compile(r"PDG\d+\.\d+\.metadata\.tsv"),
kkonganti@17:         suffix=".metadata.tsv",
kkonganti@17:         overwrite=overwrite,
kkonganti@17:         release=release,
kkonganti@17:     )
kkonganti@17: 
kkonganti@17:     # Save cluster to target mapping
kkonganti@17:     dl_pdg(
kkonganti@17:         db_path=db_path,
kkonganti@17:         url="/".join([ncbi_pathogens_loc, "Clusters"]),
kkonganti@17:         regex=re.compile(r"PDG\d+\.\d+\.reference_target\.cluster_list\.tsv"),
kkonganti@17:         suffix="reference_target\.cluster_list\.tsv",
kkonganti@17:         overwrite=overwrite,
kkonganti@17:         release=release,
kkonganti@17:     )
kkonganti@17: 
kkonganti@17:     # Create accs.txt for dataformat to fetch required ACC fields
kkonganti@17:     accs_file = os.path.join(dest_dir, "accs_all.txt")
kkonganti@17:     with open(file, "r") as pdg_metadata_fh:
kkonganti@17:         with open(accs_file, "w") as accs_fh:
kkonganti@17:             for line in pdg_metadata_fh.readlines():
kkonganti@17:                 if re.match(r"^#", line) or line in ["\n", "\n\r", "\r"]:
kkonganti@17:                     continue
kkonganti@17:                 cols = line.strip().split("\t")
kkonganti@17:                 asm_acc = cols[9]
kkonganti@17:                 accs_fh.write(f"{asm_acc}\n") if (asm_acc != "NULL") else None
kkonganti@17:         accs_fh.close()
kkonganti@17:     pdg_metadata_fh.close()
kkonganti@17: 
kkonganti@17:     logging.info("Finished writing accessions for dataformat tool.")
kkonganti@17: 
kkonganti@17: 
kkonganti@17: if __name__ == "__main__":
kkonganti@17:     main()