pyhiv package

Subpackages

• pyhiv.align package
  • Submodules
  • pyhiv.align.align_with_reference module
    • align_with_references()
    • calculate_alignment_score()
    • process_alignment()
  • pyhiv.align.famsa module
    • pyfamsa_align()
  • Module contents
• pyhiv.loading package
  • Submodules
  • pyhiv.loading.read_fastas module
    • read_input_fastas()
  • Module contents
    • read_input_fastas()
    • validate_reference_paths()
• pyhiv.report package
  • Submodules
  • pyhiv.report.constants module
    • GenePanelConfig
      • GenePanelConfig.ALIGNMENT_CLEARANCE
      • GenePanelConfig.BOTTOM_MARGIN
      • GenePanelConfig.NON_K03455_X_MAX_DEFAULT
      • GenePanelConfig.REV_CONNECTOR
      • GenePanelConfig.TAT_CONNECTOR
      • GenePanelConfig.TOP_MARGIN
      • GenePanelConfig.X_PAD_MIN
      • GenePanelConfig.Y_SCALE
    • K03455Config
      • K03455Config.DEFAULT_K03455_OFFSETS
      • K03455Config.K03455_NUMERIC_OFFSETS
      • K03455Config.TARGET_REGIONS
      • K03455Config.Y_POSITIONS
      • K03455Config.get_k03455_offsets()
    • MetadataConfig
      • MetadataConfig.FONTSIZE
      • MetadataConfig.INFO_TOP_Y
      • MetadataConfig.TITLE_Y
      • MetadataConfig.WRAP
    • NumericOffsets
      • NumericOffsets.DEFAULT_OFFSETS
      • NumericOffsets.GENE_OFFSET_MAP
      • NumericOffsets.get_offsets()
    • PageLayout
      • PageLayout.FIGSIZE
      • PageLayout.GRID_HEIGHT_RATIOS
      • PageLayout.HSPACE
  • pyhiv.report.pdf_generator module
    • render_sequence_page()
  • pyhiv.report.reporter module
    • PyHIVReporter
      • PyHIVReporter.generate_report()
  • pyhiv.report.utils module
    • build_alignment_path()
    • build_ref_to_alignment_map()
    • canon_label()
    • first_last_nongap_idx()
    • get_numeric_offsets_non_special()
    • is_special_reference()
    • normalize_features()
    • normalize_present_regions()
    • parse_features()
    • parse_present_regions()
    • project_features_to_alignment()
    • read_alignment_fasta()
    • ungap()
  • pyhiv.report.visualization module
    • plot_gene_axes()
  • Module contents
    • GenePanelConfig
      • GenePanelConfig.ALIGNMENT_CLEARANCE
      • GenePanelConfig.BOTTOM_MARGIN
      • GenePanelConfig.NON_K03455_X_MAX_DEFAULT
      • GenePanelConfig.REV_CONNECTOR
      • GenePanelConfig.TAT_CONNECTOR
      • GenePanelConfig.TOP_MARGIN
      • GenePanelConfig.X_PAD_MIN
      • GenePanelConfig.Y_SCALE
    • K03455Config
      • K03455Config.DEFAULT_K03455_OFFSETS
      • K03455Config.K03455_NUMERIC_OFFSETS
      • K03455Config.TARGET_REGIONS
      • K03455Config.Y_POSITIONS
      • K03455Config.get_k03455_offsets()
    • MetadataConfig
      • MetadataConfig.FONTSIZE
      • MetadataConfig.INFO_TOP_Y
      • MetadataConfig.TITLE_Y
      • MetadataConfig.WRAP
    • NumericOffsets
      • NumericOffsets.DEFAULT_OFFSETS
      • NumericOffsets.GENE_OFFSET_MAP
      • NumericOffsets.get_offsets()
    • PageLayout
      • PageLayout.FIGSIZE
      • PageLayout.GRID_HEIGHT_RATIOS
      • PageLayout.HSPACE
    • PyHIVReporter
      • PyHIVReporter.generate_report()
    • build_alignment_path()
    • build_ref_to_alignment_map()
    • canon_label()
    • first_last_nongap_idx()
    • get_numeric_offsets_non_special()
    • is_special_reference()
    • normalize_features()
    • normalize_present_regions()
    • parse_features()
    • parse_present_regions()
    • plot_gene_axes()
    • project_features_to_alignment()
    • read_alignment_fasta()
    • render_sequence_page()
    • ungap()
• pyhiv.split package
  • Submodules
  • pyhiv.split.split module
    • get_gene_region()
    • get_present_gene_regions()
    • map_ref_coords_to_alignment()
  • Module contents

Submodules

pyhiv.cli module

PyHIV Command Line Interface

pyhiv.cli.count_fasta_files(directory)

Count FASTA files in the input directory.

pyhiv.cli.validate_n_jobs(ctx, param, value)

Validate that n_jobs is positive if provided.

pyhiv.config module

pyhiv.config.get_reference_base_dir()

Return the root directory for reference genomes.

Return type:

Path

pyhiv.config.get_reference_paths(base_dir=None)

Return all key reference paths derived from the base directory.

Parameters:

base_dir (Path | None)

Return type:

dict[str, Path]

pyhiv.config.validate_reference_paths(paths=None)

Ensure all required reference files and directories exist.

Parameters:

paths (dict[str, Path] | None)

Module contents

pyhiv.PyHIV(fastas_dir, subtyping=True, splitting=True, output_dir=None, n_jobs=None, reporting=True)

Main function to run the PyHIV pipeline. It aligns the user sequences with the reference sequences and saves the best alignment in a fasta file. If subtyping is True, it aligns the user sequences with the reference sequences from the HIV-1 subtyping tool. If splitting is True, it splits the user sequences into gene regions and saves them in specific folders. It also saves a final table with the results. If reporting is True, it generates a PDF report with visualizations.

Parameters:

• fastas_dir (str)

• subtyping (bool)

• splitting (bool)

• output_dir (str | None)

• n_jobs (int | None)

• reporting (bool)