geneml 1.0.0__py3-none-any.whl

geneml/__init__.py

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+from ._version import __version__
+
+__all__ = ["__version__"]

geneml/_version.py

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+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '1.0.0'
+__version_tuple__ = version_tuple = (1, 0, 0)
+
+__commit_id__ = commit_id = None

geneml/args.py

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+import argparse
+import os
+import re
+from argparse import Namespace
+
+from geneml import __version__
+from geneml.params import Strand
+
+
+def positive_int(value) -> int:
+    """Validate that input is a positive integer.
+
+    Args:
+        value: Input value to validate.
+
+    Returns:
+        The validated integer value.
+    """
+    ivalue = int(value)
+    if ivalue < 1:
+        raise argparse.ArgumentTypeError(f"Must be a positive integer, got {value}.")
+    return ivalue
+
+
+def unit_float(value) -> float:
+    """Validate that input is a float in the range [0, 1].
+
+    Args:
+        value: Input value to validate.
+
+    Returns:
+        The validated float value.
+    """
+    fvalue = float(value)
+    if not (0.0 <= fvalue <= 1.0):
+        raise argparse.ArgumentTypeError(f"Must be between 0 and 1, got {value}.")
+    return fvalue
+
+
+def gene_score(value) -> str | float:
+    """Validate gene score as 'dynamic' or a float in the range [0, 1].
+
+    Args:
+        value: Input value to validate.
+
+    Returns:
+        The string 'dynamic' or a validated float value.
+    """
+    if value == 'dynamic':
+        return value
+    try:
+        return unit_float(value)
+    except argparse.ArgumentTypeError as e:
+        raise argparse.ArgumentTypeError(
+            f"Must be a float between 0 and 1, or 'dynamic', got {value}."
+            ) from e
+
+
+def gene_id_prefix(value: str) -> str:
+    """Validate a gene ID prefix for output identifiers.
+
+    Args:
+        value: Prefix value to validate.
+
+    Returns:
+        The validated prefix.
+    """
+    if not value:
+        raise argparse.ArgumentTypeError("Gene ID prefix must not be empty.")
+    if re.fullmatch(r'[A-Za-z0-9_.-]+', value) is None:
+        raise argparse.ArgumentTypeError(
+            "Gene ID prefix may contain only letters, digits, '.', '_', and '-'."
+        )
+    return value
+
+
+def get_basepath(inpath: str, outpath: str | None) -> str:
+    """Resolve the base output path without extension.
+
+    Args:
+        inpath: Input sequence path.
+        outpath: Optional explicit output path.
+
+    Returns:
+        Output base path without file extension.
+    """
+    if outpath:
+        return os.path.splitext(outpath)[0]
+    return os.path.splitext(inpath)[0]
+
+
+def check_input_path(parser, path: str, label: str) -> None:
+    """Validate that an input path exists and is readable.
+
+    Args:
+        parser: Argument parser used to report validation errors.
+        path: Path to validate.
+        label: Human-readable argument label for error messages.
+
+    Returns:
+        None.
+    """
+    if not os.path.exists(path):
+        parser.error(f"{label} does not exist: {path}")
+    if not os.path.isfile(path):
+        parser.error(f"{label} is not a file: {path}")
+    if not os.access(path, os.R_OK):
+        parser.error(f"{label} is not readable: {path}")
+
+
+def check_output_path(parser, path: str, label: str) -> None:
+    """Validate that an output path can be written.
+
+    Args:
+        parser: Argument parser used to report validation errors.
+        path: Path to validate.
+        label: Human-readable argument label for error messages.
+
+    Returns:
+        None.
+    """
+    if os.path.isdir(path):
+        parser.error(f"{label} points to a directory, not a file: {path}")
+
+    parent_dir = os.path.dirname(os.path.abspath(path)) or os.curdir
+    if not os.path.exists(parent_dir):
+        parser.error(f"Parent directory for {label} does not exist: {parent_dir}")
+    if not os.path.isdir(parent_dir):
+        parser.error(f"Parent path for {label} is not a directory: {parent_dir}")
+
+    if os.path.exists(path):
+        if not os.path.isfile(path):
+            parser.error(f"{label} is not a regular file: {path}")
+        if not os.access(path, os.W_OK):
+            parser.error(f"{label} is not writable: {path}")
+    elif not os.access(parent_dir, os.W_OK):
+        parser.error(f"Parent directory for {label} is not writable: {parent_dir}")
+
+
+def check_paths(parser, args) -> None:
+    """Validate input, output, and log file paths.
+
+    Args:
+        parser: Argument parser used to report validation errors.
+        args: Parsed CLI arguments namespace.
+
+    Returns:
+        None.
+    """
+    basepath = get_basepath(args.sequence, args.output)
+
+    check_input_path(parser, args.sequence, "sequence path")
+    if args.model:
+        check_input_path(parser, args.model, "--model")
+
+    check_output_path(
+        parser,
+        args.output if args.output else ''.join([basepath, '.gff3']),
+        "annotation output path",
+    )
+    check_output_path(parser, ''.join([basepath, '.log']), "log output path")
+
+    if args.genes:
+        check_output_path(parser, args.genes, "--genes")
+    if args.proteins:
+        check_output_path(parser, args.proteins, "--proteins")
+
+
+def check_args(parser, args) -> None:
+    """Validate combinations of parsed CLI arguments and check file paths.
+
+    Args:
+        parser: Argument parser used to report validation errors.
+        args: Parsed CLI arguments namespace.
+
+    Returns:
+        None.
+    """
+    if args.model and not args.context_length:
+        parser.error("--context-length is required when using a custom model.")
+    if args.min_exon_size > args.max_exon_size:
+        parser.error(f"--min-exon-size ({args.min_exon_size}) cannot exceed "
+                     f"--max-exon-size ({args.max_exon_size}).")
+    if args.min_intron_size > args.max_intron_size:
+        parser.error(f"--min-intron-size ({args.min_intron_size}) cannot exceed "
+                     f"--max-intron-size ({args.max_intron_size}).")
+    check_paths(parser, args)
+
+
+def parse_args(argv=None) -> Namespace:
+    """Parse and validate command-line arguments for geneML.
+
+    Args:
+        argv: Optional argument list. If None, arguments are read from sys.argv.
+
+    Returns:
+        Parsed and validated CLI arguments.
+    """
+    version_string = f"geneML {__version__}"
+    parser = argparse.ArgumentParser(description=version_string, add_help=False)
+
+    parser.add_argument('-h', '--help',
+                        action='help',
+                        help="Show this help message and exit.")
+    parser.add_argument('--version',
+                        action='version',
+                        version=version_string,
+                        help="Show version number and exit.")
+    parser.add_argument('sequence',
+                        type=str,
+                        help="Sequence file in FASTA/GenBank/EMBL format.")
+    parser.add_argument('-o', '--output',
+                        type=str,
+                        help="Gene annotations output path (default: based on input filename).")
+    parser.add_argument('-g', '--genes',
+                        type=str,
+                        help="Gene sequences output path (default: None).")
+    parser.add_argument('-p', '--proteins',
+                        type=str,
+                        help="Protein sequences output path (default: None).")
+    parser.add_argument('--gene-id-prefix',
+                    type=gene_id_prefix,
+                    help=("Prefix for gene IDs in output (default: None)."))
+    parser.add_argument('-m', '--model',
+                        type=str,
+                        help="Path to model file (default: models/geneML_default.keras).")
+    parser.add_argument('-cl', '--context-length',
+                        type=positive_int,
+                        help="Context length of the model.")
+    parser.add_argument('-c', '--cores',
+                        type=positive_int,
+                        help="Number of cores to use for processing (default: all available).")
+
+    advanced = parser.add_argument_group("advanced options")
+    advanced.add_argument('-v', '--verbose',
+                          action='store_true',
+                          help="Enable verbose mode.")
+    advanced.add_argument('-d', '--debug',
+                          action='store_true',
+                          help="Enable debug mode.")
+    advanced.add_argument('--cpu-only',
+                          action='store_true',
+                          help="Use CPU only for inference, disable GPU usage.")
+    advanced.add_argument('--strand',
+                          type=str,
+                          choices=[x.value for x in Strand],
+                          default='both',
+                          help="On which strand to predict genes (default: %(default)s).")
+    advanced.add_argument('--contigs-filter',
+                          type=str,
+                          help="Run only on selected contigs (comma separated string).")
+    advanced.add_argument('--write-raw-scores',
+                          action='store_true',
+                          help=("Instead of running gene calling, "
+                                "output the raw model scores as a .seg file."))
+    advanced.add_argument('--max-transcripts',
+                          type=positive_int,
+                          default=5,
+                          help="Maximum number of transcripts per gene (default: %(default)s).")
+    advanced.add_argument('--allow-opposite-strand-overlaps',
+                          choices=['true', 'false'],
+                          default='true',
+                          help=("Predict overlapping genes on opposite strands "
+                                "(default: %(default)s)."))
+    advanced.add_argument('--min-gene-score',
+                          type=gene_score,
+                          default='dynamic',
+                          help=("Minimum gene score for gene reporting. "
+                                "Can be a float value or 'dynamic' (default: %(default)s). "
+                                "Dynamic mode requires >=100,000 bp total input."))
+    advanced.add_argument('--min-exon-size',
+                          type=positive_int,
+                          default=1,
+                          help="Minimum exon size (default: %(default)s).")
+    advanced.add_argument('--max-exon-size',
+                          type=positive_int,
+                          default=30000,
+                          help="Maximum exon size (default: %(default)s).")
+    advanced.add_argument('--min-intron-size',
+                          type=positive_int,
+                          default=10,
+                          help="Minimum intron size (default: %(default)s).")
+    advanced.add_argument('--max-intron-size',
+                          type=positive_int,
+                          default=400,
+                          help="Maximum intron size (default: %(default)s).")
+    advanced.add_argument('--cds-start-min-score',
+                          type=unit_float,
+                          default=0.01,
+                          help=("Minimum model score for considering a CDS start "
+                                "(default: %(default)s)."))
+    advanced.add_argument('--cds-end-min-score',
+                          type=unit_float,
+                          default=0.01,
+                          help=("Minimum model score for considering a CDS end "
+                                "(default: %(default)s)."))
+    advanced.add_argument('--exon-start-min-score',
+                          type=unit_float,
+                          default=0.01,
+                          help=("Minimum model score for considering an exon start "
+                                "(default: %(default)s)."))
+    advanced.add_argument('--exon-end-min-score',
+                          type=unit_float,
+                          default=0.01,
+                          help=("Minimum model score for considering an exon end "
+                                "(default: %(default)s)."))
+    advanced.add_argument('--gene-candidates',
+                          type=positive_int,
+                          default=5000,
+                          help=("Maximum number of gene candidates to consider per locus "
+                                "(default: %(default)s)."))
+
+    args = parser.parse_args(argv)
+    check_args(parser, args)
+
+    return args