AAFTF 0.7.0b2__py3-none-any.whl

AAFTF/AAFTF_main.py

@@ -0,0 +1,903 @@
+#!/usr/bin/env python3
+"""AAFTF main framework for submodule run."""
+
+# note structure of code taken from poretools
+# https://github.com/arq5x/poretools/blob/master/poretools/poretools_main.py
+
+import argparse as ap
+import sys
+
+# AAFTF imports
+from AAFTF.__version__ import __version__, get_version  # noqa: E402
+from AAFTF.utility import status
+
+try:
+    myversion = get_version()
+except Exception:
+    # Fallback to hardcoded version if git isn't available
+    myversion = __version__
+
+
+ALIAS_MAP = {
+    "trim_reads": "trim",
+    "read_trim": "trim",
+    "filter_reads": "filter",
+    "read_filter": "filter",
+    "asm": "assemble",
+    "spades": "assemble",
+    "vectorscreen": "vecscreen",
+    "vector_blast": "vecscreen",
+    "ncbi_fcs": "fcs_screen",
+    "ncbi_fcs-screen": "fcs_screen",
+    "ncbi_fcs-gx": "fcs_gx_purge",
+    "ncbi_fcs_gx": "fcs_gx_purge",
+    "gx": "fcs_gx_purge",
+    "purge": "sourpurge",
+    "dedup": "rmdup",
+    "pilon": "polish",
+    "polca": "polish",
+    "stats": "assess",
+    "fix": "fix_tbl",
+    "mito_asm": "mito",
+    "mitochondria": "mito",
+    "coverage": "depth",
+    "cov": "depth",
+    "configure": "download",
+    "install": "download",
+    "download_db": "download",
+    "setup": "download",
+}
+
+
+def run_subtool(parser, args):
+    """Run the subtool of the AAFTF pipeline."""
+    command = ALIAS_MAP.get(args.command, args.command)
+    if command == "trim":
+        import AAFTF.trim as submodule
+    elif command == "filter":
+        import AAFTF.filter as submodule
+    elif command == "assemble":
+        import AAFTF.assemble as submodule
+    elif command == "vecscreen":
+        import AAFTF.vecscreen as submodule
+    elif command == "fcs_screen":
+        import AAFTF.fcs_screen as submodule
+    elif command == "fcs_gx_purge":
+        import AAFTF.fcs_gx_purge as submodule
+    elif command == "sourpurge":
+        import AAFTF.sourpurge as submodule
+    elif command == "rmdup":
+        import AAFTF.rmdup as submodule
+    elif command == "polish":
+        import AAFTF.polish as submodule
+    elif command == "assess":
+        import AAFTF.assess as submodule
+    elif command == "sort":
+        import AAFTF.sort as submodule
+    elif command == "pipeline":
+        import AAFTF.pipeline as submodule
+    elif command == "mito":
+        import AAFTF.mito as submodule
+    elif command == "fix_tbl":
+        import AAFTF.fix_tbl as submodule
+    elif command == "depth":
+        import AAFTF.depth as submodule
+    elif command == "download":
+        import AAFTF.download as submodule
+    else:
+        parser.parse_args("")
+        return
+    # run the chosen submodule.
+    submodule.run(parser, args)
+
+
+class ArgumentParserWithDefaults(ap.ArgumentParser):
+    """Argument parsing top level."""
+
+    def __init__(self, *args, **kwargs):
+        """Init function for ArgumentParser."""
+        super().__init__(*args, **kwargs)
+        self.add_argument("-q", "--quiet", help="Do not output warnings to stderr", action="store_true", dest="quiet")
+
+    def error(self, message):
+        """Error message passing from argument passing."""
+        sys.stderr.write(f"error: {message}\n")
+        self.print_help()
+        sys.exit(2)
+
+
+def main():
+    """Present the main AAFTF module submenus."""
+    #########################################
+    # create the top-level parser
+    #########################################
+    parser = ap.ArgumentParser(prog="AAFTF", formatter_class=ap.ArgumentDefaultsHelpFormatter)
+    parser.add_argument("-q", "--quiet", help="Do not output warnings to stderr", action="store_true", dest="quiet")
+    parser.add_argument("-v", "--version", help="Installed AAFTF version", action="version", version="%(prog)s " + str(myversion))
+
+    subparsers = parser.add_subparsers(title="[sub-commands]", dest="command", parser_class=ArgumentParserWithDefaults)
+
+    #########################################
+    # setup / database download
+    #########################################
+    parser_download = subparsers.add_parser(
+        "download",
+        aliases=["configure", "install", "download_db", "setup"],
+        description="Download reference databases to a persistent directory.",
+        help="Download AAFTF reference databases",
+    )
+    parser_download.add_argument(
+        "--AAFTF_DB",
+        type=str,
+        required=False,
+        help="Path to AAFTF database directory. Defaults to $AAFTF_DB environment variable.",
+    )
+    parser_download.add_argument(
+        "--force",
+        action="store_true",
+        help="Re-download files even if they already exist",
+    )
+    parser_download.add_argument(
+        "--skip-core",
+        action="store_true",
+        help="Skip downloading core contamination databases (UniVec, PhiX, contaminants, mitochondria)",
+    )
+    parser_download.add_argument(
+        "--skip-sourmash",
+        action="store_true",
+        help="Skip downloading sourmash taxonomy databases",
+    )
+    parser_download.add_argument(
+        "--sourdb-type",
+        type=str,
+        default="all",
+        choices=["gbk", "gtdb", "gtdbrep", "all"],
+        dest="sourdb_type",
+        help="Which sourmash database(s) to download (default: all)",
+    )
+    parser_download.add_argument(
+        "--skip-fcs",
+        action="store_true",
+        help="Skip downloading NCBI FCS-adaptor resources",
+    )
+    parser_download.add_argument("-v", "--debug", action="store_true", help="Provide debugging messages")
+    parser_download.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    #########################################
+    # create the individual tool parsers
+    #########################################
+
+    ##########
+    # trim
+    ##########
+    # arguments
+    # --method bbduk*, trimmomatic, fastp
+    # --trimmomatic: arguments are path to JAR or application respectively
+    # assume java is PATH already for trimmomatic
+    # -o / --outdir: write outdir
+    # -p / --prefix: outfile prefix
+    # -ml / --minlen: min read length
+    # --avgqual (default 10)
+    # read info, either paired data are required or singleton
+    # --left: left or forward reads
+    # --right: right or reverse reads
+    #
+    # --merge: merge reads in fastp
+
+    parser_trim = subparsers.add_parser("trim", aliases=["trim_reads", "read_trim"], description="This command trims reads in FASTQ format to " + "remove low quality reads and trim adaptor sequences", help="Trim FASTQ input reads")
+
+    parser_trim.add_argument("-o", "--out", type=str, required=False, dest="basename", help="Output basename, default to base name of --left reads")
+
+    parser_trim.add_argument("-c", "--cpus", type=int, metavar="cpus", required=False, default=1, help="Number of CPUs/threads to use.")
+
+    parser_trim.add_argument("-ml", "--minlen", type=int, default=75, required=False, help="Minimum read length after trimming, default: 75")
+
+    parser_trim.add_argument("-l", "--left", type=str, required=True, help="left/forward reads of paired-end FASTQ or single-end FASTQ.")
+
+    parser_trim.add_argument("-r", "--right", type=str, required=False, help="right/reverse reads of paired-end FASTQ.")
+
+    parser_trim.add_argument("-aq", "--avgqual", type=int, default=10, required=False, help="Average Quality of reads must be > than this, default: 10")
+
+    parser_trim.add_argument("--dedup", action="store_true", required=False, help="Run fastp deuplication of fastq reads (default uses ~4gb mem)" + " default: false")
+
+    parser_trim.add_argument("--cutfront", action="store_true", required=False, help="Run fastp 5' trimming based on quality. " + "default: false. \n" + "WARNING: this operation will interfere deduplication for SE data")
+
+    parser_trim.add_argument("--cuttail", action="store_true", required=False, help="Run fastp 3' trimming based on quality. " + "default: false.\n" + "WARNING: this operation will interfere deduplication for SE data")
+
+    parser_trim.add_argument("--cutright", action="store_true", required=False, help="Run fastp move a sliding window from front to tail, " + "if meet one window with mean quality < threshold. \n" + "default: false.\n" + "WARNING: this operation will interfere deduplication for SE data")
+
+    parser_trim.add_argument("-v", "--debug", action="store_true", help="Provide debugging messages")
+
+    parser_trim.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    parser_trim.add_argument("--method", default="bbduk", choices=["bbduk", "trimmomatic", "fastp"], help="Program to use for adapter trimming")
+
+    parser_trim.add_argument("-m", "--memory", type=int, dest="memory", required=False, help="Max Memory (in GB)")
+
+    parser_trim.add_argument("--merge", action="store_true", help="Merge paired end reads when running fastp")
+
+    parser_trim.add_argument("--prefix", type=str, required=False, help="Prefix for outfiles")
+
+    tool_group = parser_trim.add_mutually_exclusive_group(required=False)
+
+    tool_group.add_argument("--trimmomatic", "--jar", metavar="trimmomatic_jar", type=str, required=False, help="Trimmomatic JAR path")
+    trimmomatic_group = parser_trim.add_argument_group(title="Trimmomatic options", description="Trimmomatic trimming options")
+
+    trimmomatic_group.add_argument("--trimmomatic_adaptors", default="TruSeq3-PE.fa", help="Trimmomatic adaptor file, default: TruSeq3-PE.fa")
+
+    trimmomatic_group.add_argument("--trimmomatic_clip", default="ILLUMINACLIP:%s:2:30:10", help="Trimmomatic clipping, " + "default: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10")
+
+    trimmomatic_group.add_argument("--trimmomatic_leadingwindow", default="3", type=int, help="Trimmomatic window processing arguments, default: LEADING:3")
+
+    trimmomatic_group.add_argument("--trimmomatic_trailingwindow", default="3", type=int, help="Trimmomatic window processing arguments, default: TRAILING:3")
+
+    trimmomatic_group.add_argument("--trimmomatic_slidingwindow", default="4:15", type=str, help="Trimmomatic window processing arguments, " + "default: SLIDINGWINDOW:4:15")
+
+    trimmomatic_group.add_argument("--trimmomatic_quality", default="phred33", help="Trimmomatic quality encoding -phred33 or phred64")
+
+    ##########
+    # mito-asm assembly mitochondrial genome
+    ##########
+
+    parser_mito = subparsers.add_parser("mito", aliases=["mito_asm", "mitochondria"], description="De novo assembly of mitochondrial genome using " + "NOVOplasty, takes PE Illumina adapter trimmed data.", help="De novo assembly of mitochondrial genome")
+    parser_mito.add_argument("-l", "--left", required=True, help="Left (Forward) reads")
+
+    parser_mito.add_argument("-r", "--right", required=True, help="Right (Reverse) reads")
+
+    parser_mito.add_argument("-o", "--out", type=str, required=True, help="Output FASTA file for mitochondrial genome")
+
+    parser_mito.add_argument("--minlen", default=10000, type=int, help="Minimum expected genome size")
+
+    parser_mito.add_argument("--maxlen", default=100000, type=int, help="Maximum expected genome size")
+
+    parser_mito.add_argument("-s", "--seed", required=False, help="Seed sequence, ie related mitochondrial genome." + "default: A. nidulans")
+
+    parser_mito.add_argument("--starting", required=False, help="FASTA file of start sequence, rotate genome to, default COB")
+
+    parser_mito.add_argument("--reference", required=False, help="Run NOVOplasty in reference mode")
+
+    parser_mito.add_argument("-w", "--workdir", "--tmpdir", type=str, dest="workdir", required=False, help="Temporary directory to store datafiles and processes in")
+
+    parser_mito.add_argument("-v", "--debug", action="store_true", help="Provide debugging messages")
+
+    parser_mito.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    ##########
+    # filter
+    ##########
+    # arguments
+    # -i / --indir:  input dir
+    # -o / --out: in fastq reads and output prefix
+    # -a / --screen_accessions: screening sequence GenBank accessions
+    # -u / --screen_urls: screening sequence URLs (fasta format)
+    # --debug: print debug messages and do no remove contamdb BAM file
+    # read info, either paired data are required or singleton
+    # --left: left or forward reads
+    # --right: right or reverse reads
+    # --single: single unpaired reads
+    # or value from --prefix
+    # --aligner: bbduk bwa, bowtie2, minimap for read alignment to contamdb
+
+    parser_filter = subparsers.add_parser("filter", aliases=["filter_reads", "read_filter"], description="Filter reads which match " + "contaminant databases such as phiX", help="Filter contaminanting reads")
+
+    parser_filter.add_argument("-w", "--workdir", type=str, help="temp directory")
+
+    parser_filter.add_argument("-c", "--cpus", type=int, metavar="cpus", required=False, default=1, help="Number of CPUs/threads to use.")
+
+    parser_filter.add_argument("-o", "--out", dest="basename", type=str, required=False, help="Output basename")
+
+    parser_filter.add_argument("-v", "--debug", action="store_true", help="Provide debugging messages and do not remove contamdb " + "matching BAM file")
+
+    parser_filter.add_argument("-a", "--screen_accessions", type=str, nargs="*", help="Genbank accession number(s) to screen out from initial reads.")
+
+    parser_filter.add_argument("-u", "--screen_urls", type=str, nargs="*", help="URLs to download and screen out initial reads.")
+
+    parser_filter.add_argument("-s", "--screen_local", type=str, nargs="+", help="Local FASTA file(s) to use contamination screen")
+
+    parser_filter.add_argument("-l", "--left", required=True, help="Left (Forward) reads")
+
+    parser_filter.add_argument("-r", "--right", required=False, help="Right (Reverse) reads")
+
+    parser_filter.add_argument("--AAFTF_DB", type=str, required=False, help="Path to AAFTF resources, defaults to $AAFTF_DB")
+
+    parser_filter.add_argument("--aligner", default="bbduk", choices=["bbduk", "bowtie2", "bwa", "minimap2"], help="Aligner to use to map reads to contamination database")
+
+    parser_filter.add_argument("-m", "--memory", type=int, dest="memory", required=False, help="Max Memory (in GB)")
+
+    parser_filter.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    ##########
+    # assemble
+    ##########
+    # arguments
+    # -i / --indir:  input folder
+    # -o / --outdir: output folder
+    # -p / --prefix: input/outfile prefix
+    # --paired or --unpaired
+    # --spades
+    # --merged for merged reads
+    # --tmpdir: tempdir for spades
+
+    parser_asm = subparsers.add_parser("assemble", aliases=["asm", "spades"], description="Run assembler on cleaned reads", help="Assemble reads")
+
+    parser_asm.add_argument("--method", type=str, choices=["spades", "dipspades", "megahit", "unicycler"], required=False, default="spades", help="Assembly method: spades, dipspades, megahit, unicycler. Default: spades")
+
+    parser_asm.add_argument(
+        "-o",
+        "--out",
+        type=str,
+        required=True,  # think about sensible replacement in future
+        help="Output assembly FASTA",
+    )
+
+    parser_asm.add_argument("-w", "--workdir", type=str, dest="workdir", help="assembly output directory")
+
+    parser_asm.add_argument("-c", "--cpus", type=int, metavar="cpus", required=False, default=1, help="Number of CPUs/threads to use.")
+
+    parser_asm.add_argument("-m", "--memory", type=str, dest="memory", required=False, default="32", help="Memory (in GB) setting for SPAdes. Default is 32gb")
+
+    parser_asm.add_argument("-l", "--left", required=False, help="Left (Forward) reads")
+
+    parser_asm.add_argument("-r", "--right", required=False, help="Right (Reverse) reads")
+    parser_asm.add_argument("-lr", "--longreads", required=False, help="Long Read fastq (pacbio or ONT)")
+    parser_asm.add_argument("--single", "--merged", required=False, dest="merged", help="Merged reads from flash or fastp or just single end reads")
+
+    parser_asm.add_argument("--careful", required=False, action="store_true", default=True, help="Run --careful mode in spades (Default)", dest="careful")
+
+    parser_asm.add_argument("--no-careful", required=False, action="store_false", default=True, dest="careful")
+
+    parser_asm.add_argument("--isolate", required=False, action="store_true", dest="isolate", help="Run in isolate mode (default)")
+
+    parser_asm.add_argument("--no-isolate", required=False, action="store_false", dest="isolate", help="Don't run --isolate mode")
+
+    parser_asm.add_argument("-v", "--debug", action="store_true", help="Print Spades stdout to terminal")
+
+    parser_asm.add_argument("--tmpdir", type=str, required=False, help="Assembler temporary dir")
+
+    parser_asm.add_argument("--assembler_args", action="append", required=False, help="Additional SPAdes/Megahit arguments")
+
+    parser_asm.add_argument("--haplocontigs", dest="haplocontigs", default=False, action="store_true", help="For dipSPAdes take the haplocontigs file")
+
+    parser_asm.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    ##########
+    # vecscreen
+    ##########
+    # arguments
+    # -i / --input:  input assembly file
+    # -o / --outfile: output cleaned assembly
+    # --prefix: Prefix for output / temp files
+    # --tmpdir
+    # --pid / percent_id
+
+    parser_vecscreen = subparsers.add_parser("vecscreen", aliases=["vectorscreen", "vector_blast"], description="Screen contigs for vector and common contaminantion", help="BLASTN Vector and Contaminant Screening of contigs")
+
+    parser_vecscreen.add_argument("-c", "--cpus", type=int, metavar="cpus", default=1, help="Number of CPUs/threads to use.")
+
+    parser_vecscreen.add_argument("-i", "--input", "--infile", type=str, required=True, dest="infile", help="Input contigs or scaffold assembly")
+
+    parser_vecscreen.add_argument("-o", "--outfile", type=str, required=True, help="Output vector screened and cleaned assembly")
+
+    parser_vecscreen.add_argument("-pid", "--percent_id", type=int, required=False, help="Percent Identity cutoff for vecscreen adaptor matches")
+
+    parser_vecscreen.add_argument("--prefix", type=str, required=False, help="Prefix for tempfiles")
+
+    parser_vecscreen.add_argument("-w", "--workdir", "--tmpdir", type=str, help="Working directory to store datafiles and processes in")
+
+    parser_vecscreen.add_argument("--AAFTF_DB", type=str, required=False, help="Path to AAFTF resources, defaults to $AAFTF_DB")
+
+    parser_vecscreen.add_argument("-s", "--stringency", default="high", choices=["high", "low"], help="Stringency to filter VecScreen hits")
+
+    parser_vecscreen.add_argument("-v", "--debug", action="store_true", dest="debug", help="Provide debugging messages")
+
+    parser_vecscreen.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    ##########
+    # fcs_screen
+    ##########
+    # arguments
+    # -i / --input:  input assembly file
+    # -o / --outfile: output cleaned assembly
+    # --prefix: Prefix for output / temp files
+    # --euk - expect eukaryotic screening
+    # --prol - expect prokaryote screening
+
+    parser_fcs_screen = subparsers.add_parser("fcs_screen", aliases=["ncbi_fcs", "ncbi_fcs-screen"], description="Screen with NCBI fcs tool contigs for vector and common contaminantion", help="NCBI Foreign Contaminant Screening for Vector sequences in contigs")
+
+    parser_fcs_screen.add_argument("-i", "--input", "--infile", type=str, required=True, dest="infile", help="Input contigs or scaffold assembly")
+
+    parser_fcs_screen.add_argument("-o", "--outfile", type=str, required=True, help="Output vector screened and cleaned assembly")
+
+    parser_fcs_screen.add_argument("--prefix", type=str, required=False, help="Prefix for tempfiles")
+
+    parser_fcs_screen.add_argument("--container_engine", type=str, default="singularity", help="Container engine (singular or docker)")
+
+    parser_fcs_screen.add_argument("--image", type=str, required=False, help="Container file (or will download and look in AAFTF_DB)")
+
+    parser_fcs_screen.add_argument("-w", "--workdir", "--tmpdir", type=str, help="Working directory to store datafiles and processes in")
+
+    parser_fcs_screen.add_argument("--AAFTF_DB", type=str, required=False, help="Path to AAFTF resources, defaults to $AAFTF_DB")
+
+    parser_fcs_screen.add_argument("--prok", action="store_true", help="Run in Prokaryote matching mode")
+
+    parser_fcs_screen.add_argument("--euk", action="store_true", help="Run in Eukaryote matching mode (Default)")
+
+    parser_fcs_screen.add_argument("--fcs_script", type=str, required=False, help="location of the run_fcsadaptor.sh script (or will download automatically)")
+
+    parser_fcs_screen.add_argument("-v", "--debug", action="store_true", dest="debug", help="Provide debugging messages")
+
+    parser_fcs_screen.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    ##########
+    # fcs_gx_purge
+    ##########
+    # arguments
+    # -a / --assembly: input assembly file
+    # -o / --out: output cleaned assembly file
+    # -p / --prefix: datafile prefix and temp/output file prefix
+    # -c / --cpus: number of cpus
+    # -d / --db: path to db (this is best if is memory mapped location)
+    # -t / --taxid: ncbi taxonid (can be any node in taxonomy)
+
+    parser_fcsgx = subparsers.add_parser("fcs_gx_purge", aliases=["ncbi_fcs-gx", "ncbi_fcs_gx", "gx"], description="Purge contigs based on fcs_gx results", help="Purge contigs based on contamination search with fcs_gx")
+
+    parser_fcsgx.add_argument("-i", "--input", type=str, required=True, help="Input contigs or scaffold assembly")
+
+    parser_fcsgx.add_argument(
+        "-o",
+        "--outfile",
+        type=str,
+        required=True,  # think about sensible replacement in future
+        help="Output fcs_gx cleaned assembly",
+    )
+
+    parser_fcsgx.add_argument("--prefix", type=str, required=False, help="Prefix for tempfiles")
+
+    parser_fcsgx.add_argument("-t", "--taxid", type=int, required=False, default=4890, help="NCBI Taxonomy ID for contamaination matches, i.e. 4890 for Ascomycota")
+
+    parser_fcsgx.add_argument("-d", "--db", required=False, default="/my_tmpfs/gxdb/all", help="gxdb database path")
+
+    parser_fcsgx.add_argument("-c", "--cpus", type=int, metavar="cpus", default=1, help="Number of CPUs/threads to use.")
+
+    parser_fcsgx.add_argument("-w", "--workdir", "--tmpdir", type=str, dest="workdir", required=False, help="Temporary directory to store datafiles and processes in")
+
+    parser_fcsgx.add_argument("-v", "--debug", action="store_true", dest="debug", help="Provide debugging messages")
+
+    parser_fcsgx.add_argument("--AAFTF_DB", type=str, required=False, help="Path to AAFTF resources, defaults to $AAFTF_DB")
+
+    parser_fcsgx.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    ##########
+    # sourpurge
+    ##########
+    # arguments
+    # -i / --input: input assembly file
+    # -o / --out: output cleaned assembly file
+    # -p / --prefix: datafile prefix and temp/output file prefix
+    # -l / --left: left read of pair
+    # -r / --right: right read of pair
+    # -k / --kmer: kmer size when running sourmash (needs to match db), default '31'
+    # --sourdb_type gtdb gtdbrep gbk
+    # --tmpdir
+    # --phylum: phylum to keep
+    # -mc / --mincovpct:
+
+    parser_sour = subparsers.add_parser("sourpurge", aliases=["purge"], description="Purge contigs based on sourmash results", help="Purge contigs based on sourmash results")
+
+    parser_sour.add_argument("-i", "--input", type=str, required=True, help="Input contigs or scaffold assembly")
+
+    parser_sour.add_argument(
+        "-o",
+        "--outfile",
+        type=str,
+        required=True,  # think about sensible replacement in future
+        help="Output sourmash cleaned assembly",
+    )
+
+    parser_sour.add_argument("--prefix", type=str, required=False, help="Prefix for tempfiles")
+
+    parser_sour.add_argument("-l", "--left", required=False, help="Left (Forward) reads")
+
+    parser_sour.add_argument("-r", "--right", required=False, help="Right (Reverse) reads")
+
+    parser_sour.add_argument("-p", "--phylum", required=True, nargs="+", help="Phylum or Phyla to keep matches, i.e. Ascomycota")
+
+    parser_sour.add_argument("--sourdb", required=False, help="SourMash LCA taxonomy database (defaults to k-31)")
+
+    parser_sour.add_argument("-k", "--kmer", required=False, default="31", help="SourMash LCA kmersize when taxonomy database was built")
+
+    parser_sour.add_argument("-mc", "--mincovpct", default=5, type=int, help="Minimum percent of N50 coverage to remove")
+
+    parser_sour.add_argument("-c", "--cpus", type=int, metavar="cpus", default=1, help="Number of CPUs/threads to use.")
+
+    parser_sour.add_argument("-w", "--workdir", "--tmpdir", type=str, dest="workdir", required=False, help="Temporary directory to store datafiles and processes in")
+
+    parser_sour.add_argument("-v", "--debug", action="store_true", dest="debug", help="Provide debugging messages")
+
+    parser_sour.add_argument("--sourdb_type", default="gbk", required=False, choices=["gbk", "gtdbrep", "gtdb"], help="Which sourpurge database to use.")
+
+    parser_sour.add_argument("--AAFTF_DB", type=str, required=False, help="Path to AAFTF resources, defaults to $AAFTF_DB")
+
+    parser_sour.add_argument("--just-show-taxonomy", dest="taxonomy", action="store_true", help="Show taxonomy information and exit")
+
+    parser_sour.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    ##########
+    # rmdup
+    ##########
+
+    # -i / --input
+    # -o / --out
+    # --tmpdir
+    # --percent_id
+    # ---mincovpct
+    # -ml / --minlen
+    # --exhaustive
+    # --debug
+
+    parser_rmdup = subparsers.add_parser("rmdup", aliases=["dedup"], description="Remove duplicate contigs", help="Remove duplicate contigs")
+    parser_rmdup.add_argument("-i", "--input", type=str, required=True, help="Input Assembly fasta file(contigs or scaffolds)")
+
+    parser_rmdup.add_argument("-o", "--out", type=str, required=True, help="Output new version of assembly with " + "duplicated contigs/scaffolds removed")
+
+    parser_rmdup.add_argument("-c", "--cpus", type=int, metavar="cpus", required=False, default=1, help="Number of CPUs/threads to use.")
+
+    parser_rmdup.add_argument("-w", "--workdir", "--tmpdir", dest="workdir", type=str, required=False, help="Temporary directory to store datafiles and processes in")
+
+    parser_rmdup.add_argument("-pid", "--percent_id", type=int, dest="percent_id", required=False, default=95, help="Percent Identity used in matching contigs for redundancy")
+
+    parser_rmdup.add_argument("-pcov", "--percent_cov", type=int, dest="percent_cov", required=False, default=95, help="Coverage of contig used to decide if it is redundant")
+
+    parser_rmdup.add_argument("-ml", "--minlen", type=int, required=False, default=500, help="Minimum contig length to keep, shorter ones are dropped")
+
+    parser_rmdup.add_argument("--exhaustive", action="store_true", help="Compute overlaps for every contig, " + "otherwise only process contigs for L75 and below")
+
+    parser_rmdup.add_argument("-v", "--debug", action="store_true", help="Run rmdup in debugging mode for more output")
+
+    parser_rmdup.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    ##########
+    # polish
+    ##########
+    # arguments
+    # -i / --in: input assembly file
+    # -o / --out: output cleaned assembly
+    # --left: left fastq read file (ILLUMINA)
+    # --right: right fastq read file (ILLUMINA)
+    # --longreads: long reads (ONT/PACBIO) fastq
+    # -rp / --reads-prefix: input/outfile reads prefix
+    # --method pilon
+    # --memory: default 16
+    # --iterations: default 5
+    # --tmpdir
+    # --debug
+    # --diploid - inddicate this is a diploid organism
+
+    parser_polish = subparsers.add_parser("polish", aliases=["pilon", "polca"], description="Polish contig sequences with Pilon, POLCA, NextPolish", help="Polish contig sequences with short reads")
+
+    parser_polish.add_argument("-o", "--out", "--outfile", type=str, dest="outfile", required=False, help="Output a Polished assembly")
+
+    parser_polish.add_argument("-i", "--infile", "--input", type=str, dest="infile", required=True, help="Input contigs or scaffold assembly")
+
+    parser_polish.add_argument("-c", "--cpus", type=int, metavar="cpus", default=1, help="Number of CPUs/threads to use.")
+
+    parser_polish.add_argument("-m", "--memory", type=int, default=16, dest="memory", required=False, help="Max Memory (in GB) (default is 16gb)")
+
+    parser_polish.add_argument("-v", "--debug", action="store_true", help="Provide debugging messages")
+
+    parser_polish.add_argument("-it", "--iterations", type=int, default=5, help="Number of Polishing iterations to run (default is 5)")
+    parser_polish.add_argument("--method", type=str, choices=["pilon", "polca", "nextpolish", "racon"], required=False, default="pilon", help="Polishing method: pilon, polca, nextpolish, racon")
+
+    parser_polish.add_argument("--polca", type=str, default="polca.sh", help="polca exe path - provide full path to deal with samtools mismatch in masurca")
+
+    parser_polish.add_argument("--polca_samtools", type=str, default=None, metavar="SAMTOOLS_PATH", help="Path to a samtools binary compatible with polca.sh (e.g. samtools < 1.21). polca.sh uses 'samtools sort -f' which was removed in 1.21+; set this to an older samtools when the system default is >= 1.21.")
+
+    parser_polish.add_argument("-l", "--left", type=str, required=False, help="The name of the left/forward Illumina reads of paired-end " + "FASTQ formatted reads.")
+
+    parser_polish.add_argument("-r", "--right", type=str, required=False, help="The name of the right/reverse Illumina reads of paired-end " + "FASTQ formatted reads.")
+
+    parser_polish.add_argument("-lr", "--longreads", required=False, help="Long Read FASTQ (PacBio or ONT)")
+    parser_polish.add_argument("-w", "--workdir", "--tmpdir", type=str, dest="workdir", required=False, help="Temporary directory to store datafiles for processes")
+
+    parser_polish.add_argument("--prefix", type=str, required=False, help="Prefix for readfiles")
+
+    parser_polish.add_argument("--diploid", action="store_true", help="Run pilon in diploid mode - affects heterozygous SNP calling")
+
+    parser_polish.add_argument("--ploidy", default=1, type=int, help="Run nextpolish in specific ploidy mode - affects heterozygous SNP calling, default is 1")
+
+    parser_polish.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    ##########
+    # sort/rename FASTA headers
+    ##########
+    # arguments
+    # -i / --input: input assembly file
+    # -o / --out: output assembly file
+    # -n / --name: base name to use default=scaffolds_
+
+    parser_sort = subparsers.add_parser("sort", description="Sort contigs by length and rename FASTA headers", help="Sort contigs by length and rename FASTA headers")
+
+    parser_sort.add_argument("-i", "--input", "--infile", required=True, dest="input", help="Input genome assembly FASTA")
+
+    parser_sort.add_argument("-o", "--out", "--output", required=True, dest="out", help="Output genome assembly FASTA")
+
+    parser_sort.add_argument("-ml", "--minlen", type=int, required=False, default=0, help="Minimum contig length to keep, shorter ones are dropped")
+
+    parser_sort.add_argument("-n", "--name", "--basename", default="scaffold", dest="name", help="Basename to rename FASTA headers")
+
+    parser_sort.add_argument("-v", "--debug", action="store_true", help="Provide debugging messages")
+
+    parser_sort.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    ##########
+    # assess completeness
+    ##########
+    # arguments
+    # -i / --input: input assembly file
+    # -r / --report: report file (otherwise stdout)
+    # -t / --telomere_monomer: telomere repeat monomer pattern (default=[TAA[C]+])
+    # -n / --telomere_n_repeats: Minimum number of repeats of telomere monomer (default=2)
+
+    parser_assess = subparsers.add_parser("assess", aliases=["stats"], description="Assess completeness of genome assembly", help="Assess completeness of genome assembly")
+
+    parser_assess.add_argument("-i", "--input", "--infile", required=True, help="Input genome assembly to test completeness and " + "provide summary statistics")
+
+    parser_assess.add_argument("-r", "--report", type=str, help="Filename to save report information otherwise " + "will print to stdout")
+
+    parser_assess.add_argument("-t", "--telomere_monomer", type=str, help="Telomere repeat monomer to search for. default(TAA[C]+)", default="TAA[C]+")
+
+    parser_assess.add_argument("-n", "--telomere_n_repeat", type=int, default=2, help="Telomere minimum number of monomer repeats. (default 2)")
+
+    parser_assess.add_argument("--telomere_window", type=int, default=200, help="Number of bp to scan at each end for telomere repeats. (default 200)")
+
+    parser_assess.add_argument("-v", "--debug", action="store_true", help="Provide debugging messages")
+
+    parser_assess.add_argument("--pipe", action="store_true", help="AAFTF is running in pipeline mode")
+
+    #########
+    # fix tbl file from fcs trimmimg
+    ##########
+    # arguments
+    # -t / --table tbl file origina
+    # -o / --output output tbl file
+    # -r / --report NCBI FCS update report (a 5 column CSV file)
+
+    parser_fix = subparsers.add_parser("fix_tbl", aliases=["fix"], description="Fix NCBI tbl file from a trim report from NCBI-FCS", help="Fix the TBL file offsets from trimmimg")
+
+    parser_fix.add_argument("-t", "--table", "--infile", type=ap.FileType("rt"), required=True, help="Table format of annotation (NCBL tbl)")
+
+    parser_fix.add_argument("-r", "--report", type=ap.FileType("rt"), required=True, help="FCS report (5 column CSV)")
+
+    parser_fix.add_argument("-o", "--output", type=ap.FileType("wt"), required=True, help="Write fixed TBL file")
+
+    parser_fix.add_argument("--pipe", action="store_true", default=False, help="AAFTF is running in pipeline mode")
+
+    parser_fix.add_argument("-v", "--debug", action="store_true", dest="debug", default=False, help="Verbose/debug mode")
+
+    ##########
+    # depth of coverage
+    ##########
+    # arguments
+    # -i / --input: genome assembly FASTA
+    # -o / --out: output report file (default: coverage_stats.txt)
+    # -l / --left: forward Illumina reads
+    # -r / --right: reverse Illumina reads
+    # -lr / --longreads: long reads FASTQ (ONT/PacBio)
+    # --longread_type: minimap2 preset for long reads
+    # --illumina_preset: minimap2 preset for Illumina reads
+    # --aligner: minimap2 (default) or bwa for Illumina reads
+    # -c / --cpus
+    # -w / --workdir
+    # -v / --debug
+    # --pipe
+
+    parser_depth = subparsers.add_parser(
+        "depth",
+        aliases=["coverage", "cov"],
+        description=("Calculate depth of coverage by mapping Illumina and/or long reads " "to a genome assembly with minimap2 (or bwa), then running mosdepth " "to compute per-contig depth statistics.  Contigs with mean depth " "> assembly_mean + 3*SD are flagged as possible contaminants or " "organellar sequences."),
+        help="Calculate read depth of coverage for genome assembly",
+    )
+
+    parser_depth.add_argument(
+        "-i",
+        "--input",
+        "--infile",
+        required=True,
+        dest="input",
+        help="Input genome assembly FASTA (e.g. *.sorted.fasta)",
+    )
+
+    parser_depth.add_argument(
+        "-o",
+        "--out",
+        "--report",
+        type=str,
+        default="coverage_stats.txt",
+        dest="out",
+        help="Output coverage report file (default: coverage_stats.txt)",
+    )
+
+    parser_depth.add_argument(
+        "-l",
+        "--left",
+        required=False,
+        help="Left (Forward) Illumina reads FASTQ",
+    )
+
+    parser_depth.add_argument(
+        "-r",
+        "--right",
+        required=False,
+        help="Right (Reverse) Illumina reads FASTQ",
+    )
+
+    parser_depth.add_argument(
+        "-lr",
+        "--longreads",
+        required=False,
+        help="Long reads FASTQ (PacBio or ONT)",
+    )
+
+    parser_depth.add_argument(
+        "--longread_type",
+        default="map-ont",
+        choices=["map-ont", "map-pb", "map-hifi"],
+        dest="longread_preset",
+        help="minimap2 preset for long reads (default: map-ont)",
+    )
+
+    parser_depth.add_argument(
+        "--illumina_preset",
+        default="sr",
+        choices=["sr", "short"],
+        dest="illumina_preset",
+        help="minimap2 preset for Illumina reads (default: sr)",
+    )
+
+    parser_depth.add_argument(
+        "--aligner",
+        default="minimap2",
+        choices=["minimap2", "bwa"],
+        help="Aligner to use for Illumina reads (default: minimap2)",
+    )
+
+    parser_depth.add_argument(
+        "-c",
+        "--cpus",
+        type=int,
+        metavar="cpus",
+        required=False,
+        default=1,
+        help="Number of CPUs/threads to use.",
+    )
+
+    parser_depth.add_argument(
+        "-w",
+        "--workdir",
+        "--tmpdir",
+        type=str,
+        dest="workdir",
+        required=False,
+        help="Temporary directory to store intermediate files",
+    )
+
+    parser_depth.add_argument(
+        "-v",
+        "--debug",
+        action="store_true",
+        help="Provide debugging messages and retain intermediate files",
+    )
+
+    parser_depth.add_argument(
+        "--pipe",
+        action="store_true",
+        help="AAFTF is running in pipeline mode",
+    )
+
+    parser_depth.add_argument(
+        "--min_contig_len",
+        type=int,
+        default=500,
+        help="Minimum contig length to include in depth outlier analysis (default: 500)",
+    )
+
+    parser_depth.add_argument(
+        "--plot-format",
+        choices=["pdf", "svg", "png"],
+        default="pdf",
+        dest="plot_format",
+        help="Output format for coverage plots (default: pdf; requires matplotlib)",
+    )
+
+    parser_depth.add_argument(
+        "--no-plot",
+        action="store_true",
+        dest="no_plot",
+        help="Disable coverage plot generation",
+    )
+
+    parser_depth.add_argument(
+        "--quantize",
+        default="0:1:4:100:200:",
+        dest="quantize",
+        help="mosdepth quantize bin boundaries, colon-separated with trailing colon " "(default: 0:1:4:100:200:)",
+    )
+
+    parser_depth.add_argument(
+        "--quantize-labels",
+        default=None,
+        dest="quantize_labels",
+        metavar="LABELS",
+        help="Comma-separated labels for quantize bins " "(default: NO_COVERAGE,LOW_COVERAGE,CALLABLE,HIGH_COVERAGE,VERY_HIGH_COVERAGE " "for the default bins)",
+    )
+
+    ##########
+    # pipeline run it all
+    ##########
+    # arguments
+    # -i / --input: input assembly file
+    # -r / --report: report file (otherwise stdout)
+    # --tmpdir
+
+    parser_pipeline = subparsers.add_parser("pipeline", description="Run entire AAFTF pipeline automagically", help="Run AAFTF pipeline")
+
+    parser_pipeline.add_argument("--tmpdir", type=str, required=False, help="Assembler temporary dir")
+    parser_pipeline.add_argument("--assembler_args", action="append", required=False, help="Additional SPAdes/Megahit arguments")
+    parser_pipeline.add_argument("--method", type=str, required=False, default="spades", help="Assembly method: spades, dipspades, megahit")
+
+    parser_pipeline.add_argument("-l", "--left", type=str, required=True, help="left/forward reads of paired-end FASTQ or " + "single-end FASTQ.")
+
+    parser_pipeline.add_argument("-r", "--right", type=str, required=False, help="right/reverse reads of paired-end FASTQ.")
+
+    parser_pipeline.add_argument("-o", "--out", type=str, required=True, dest="basename", help="Output basename, default to base name of --left reads")
+
+    parser_pipeline.add_argument("-c", "--cpus", type=int, metavar="cpus", required=False, default=1, help="Number of CPUs/threads to use.")
+
+    parser_pipeline.add_argument("-m", "--memory", type=str, dest="memory", required=False, help="Memory (in GB) setting for SPAdes. Default is Auto")
+
+    parser_pipeline.add_argument("-ml", "--minlen", type=int, default=75, required=False, help="Minimum read length after trimming, default: 75")
+
+    parser_pipeline.add_argument("-a", "--screen_accessions", type=str, nargs="*", help="Genbank accession number(s) to screen out from initial reads.")
+
+    parser_pipeline.add_argument("-u", "--screen_urls", type=str, nargs="*", help="URLs to download and screen out initial reads.")
+
+    parser_pipeline.add_argument("-it", "--iterations", type=int, default=5, help="Number of Pilon Polishing iterations to run")
+
+    parser_pipeline.add_argument("-mc", "--mincontiglen", type=int, default=500, required=False, help="Minimum length of contigs to keep")
+
+    parser_pipeline.add_argument("--AAFTF_DB", type=str, required=False, help="Path to AAFTF resources, defaults to $AAFTF_DB")
+
+    parser_pipeline.add_argument("-w", "--workdir", type=str, help="temp directory")
+
+    parser_pipeline.add_argument("-v", "--debug", action="store_true", help="Provide debugging messages")
+
+    parser_pipeline.add_argument("-p", "--phylum", required=True, nargs="+", help="Phylum or Phyla to keep matches, i.e. Ascomycota")
+
+    parser_pipeline.add_argument("--sourdb", required=False, help="SourMash LCA k-31 taxonomy database")
+
+    parser_pipeline.add_argument("--mincovpct", default=5, type=int, help="Minimum percent of N50 coverage to remove")
+
+    parser_pipeline.add_argument("--pipe", action="store_true", default=False, help="AAFTF is running in pipeline mode")
+
+    # done with menu options
+    # set defaults
+    parser.set_defaults(func=run_subtool)
+
+    # process the arguments now
+    # if no args then print help and exit
+    if len(sys.argv) == 1:
+        parser.print_help(sys.stderr)
+        sys.exit(1)
+
+    args = parser.parse_args()
+
+    try:
+        status(f"Running AAFTF v{myversion}")
+        args.func(parser, args)
+    except OSError as e:
+        if e.errno != 32:  # ignore SIGPIPE
+            raise
+
+
+if __name__ == "__main__":
+    main()