Index

A

align_with_references() (in module pyhiv.align.align_with_reference)

ALIGNMENT_CLEARANCE (pyhiv.report.constants.GenePanelConfig attribute) (pyhiv.report.GenePanelConfig attribute)

B

BOTTOM_MARGIN (pyhiv.report.constants.GenePanelConfig attribute) (pyhiv.report.GenePanelConfig attribute) build_alignment_path() (in module pyhiv.report) (in module pyhiv.report.utils)

build_ref_to_alignment_map() (in module pyhiv.report) (in module pyhiv.report.utils)

C

calculate_alignment_score() (in module pyhiv.align.align_with_reference) canon_label() (in module pyhiv.report) (in module pyhiv.report.utils)

count_fasta_files() (in module pyhiv.cli)

D

DEFAULT_K03455_OFFSETS (pyhiv.report.constants.K03455Config attribute) (pyhiv.report.K03455Config attribute)

DEFAULT_OFFSETS (pyhiv.report.constants.NumericOffsets attribute) (pyhiv.report.NumericOffsets attribute)

F

FIGSIZE (pyhiv.report.constants.PageLayout attribute) (pyhiv.report.PageLayout attribute) first_last_nongap_idx() (in module pyhiv.report) (in module pyhiv.report.utils)

FONTSIZE (pyhiv.report.constants.MetadataConfig attribute) (pyhiv.report.MetadataConfig attribute)

G

GENE_OFFSET_MAP (pyhiv.report.constants.NumericOffsets attribute) (pyhiv.report.NumericOffsets attribute) GenePanelConfig (class in pyhiv.report) (class in pyhiv.report.constants) generate_report() (pyhiv.report.PyHIVReporter method) (pyhiv.report.reporter.PyHIVReporter method) get_gene_region() (in module pyhiv.split.split) get_k03455_offsets() (pyhiv.report.constants.K03455Config class method) (pyhiv.report.K03455Config class method)

get_numeric_offsets_non_special() (in module pyhiv.report) (in module pyhiv.report.utils) get_offsets() (pyhiv.report.constants.NumericOffsets class method) (pyhiv.report.NumericOffsets class method) get_present_gene_regions() (in module pyhiv.split.split) get_reference_base_dir() (in module pyhiv.config) get_reference_paths() (in module pyhiv.config) GRID_HEIGHT_RATIOS (pyhiv.report.constants.PageLayout attribute) (pyhiv.report.PageLayout attribute)

H

HSPACE (pyhiv.report.constants.PageLayout attribute) (pyhiv.report.PageLayout attribute)

I

INFO_TOP_Y (pyhiv.report.constants.MetadataConfig attribute) (pyhiv.report.MetadataConfig attribute)

is_special_reference() (in module pyhiv.report) (in module pyhiv.report.utils)

K

K03455_NUMERIC_OFFSETS (pyhiv.report.constants.K03455Config attribute) (pyhiv.report.K03455Config attribute)

K03455Config (class in pyhiv.report) (class in pyhiv.report.constants)

M

map_ref_coords_to_alignment() (in module pyhiv.split.split) MetadataConfig (class in pyhiv.report) (class in pyhiv.report.constants) module pyhiv pyhiv.align pyhiv.align.align_with_reference pyhiv.align.famsa pyhiv.cli pyhiv.config pyhiv.loading pyhiv.loading.read_fastas pyhiv.report pyhiv.report.constants pyhiv.report.pdf_generator pyhiv.report.reporter pyhiv.report.utils pyhiv.report.visualization pyhiv.split pyhiv.split.split

N

NON_K03455_X_MAX_DEFAULT (pyhiv.report.constants.GenePanelConfig attribute) (pyhiv.report.GenePanelConfig attribute) normalize_features() (in module pyhiv.report) (in module pyhiv.report.utils)

normalize_present_regions() (in module pyhiv.report) (in module pyhiv.report.utils) NumericOffsets (class in pyhiv.report) (class in pyhiv.report.constants)

P

PageLayout (class in pyhiv.report) (class in pyhiv.report.constants) parse_features() (in module pyhiv.report) (in module pyhiv.report.utils) parse_present_regions() (in module pyhiv.report) (in module pyhiv.report.utils) plot_gene_axes() (in module pyhiv.report) (in module pyhiv.report.visualization) process_alignment() (in module pyhiv.align.align_with_reference) project_features_to_alignment() (in module pyhiv.report) (in module pyhiv.report.utils) pyfamsa_align() (in module pyhiv.align.famsa) pyhiv module PyHIV() (in module pyhiv) pyhiv.align module pyhiv.align.align_with_reference module pyhiv.align.famsa module pyhiv.cli module

pyhiv.config module pyhiv.loading module pyhiv.loading.read_fastas module pyhiv.report module pyhiv.report.constants module pyhiv.report.pdf_generator module pyhiv.report.reporter module pyhiv.report.utils module pyhiv.report.visualization module pyhiv.split module pyhiv.split.split module PyHIVReporter (class in pyhiv.report) (class in pyhiv.report.reporter)

R

read_alignment_fasta() (in module pyhiv.report) (in module pyhiv.report.utils) read_input_fastas() (in module pyhiv.loading) (in module pyhiv.loading.read_fastas)

render_sequence_page() (in module pyhiv.report) (in module pyhiv.report.pdf_generator) REV_CONNECTOR (pyhiv.report.constants.GenePanelConfig attribute) (pyhiv.report.GenePanelConfig attribute)

T

TARGET_REGIONS (pyhiv.report.constants.K03455Config attribute) (pyhiv.report.K03455Config attribute) TAT_CONNECTOR (pyhiv.report.constants.GenePanelConfig attribute) (pyhiv.report.GenePanelConfig attribute)

TITLE_Y (pyhiv.report.constants.MetadataConfig attribute) (pyhiv.report.MetadataConfig attribute) TOP_MARGIN (pyhiv.report.constants.GenePanelConfig attribute) (pyhiv.report.GenePanelConfig attribute)

U

ungap() (in module pyhiv.report) (in module pyhiv.report.utils)

V

validate_n_jobs() (in module pyhiv.cli)

validate_reference_paths() (in module pyhiv.config) (in module pyhiv.loading)

W

WRAP (pyhiv.report.constants.MetadataConfig attribute) (pyhiv.report.MetadataConfig attribute)

X

X_PAD_MIN (pyhiv.report.constants.GenePanelConfig attribute) (pyhiv.report.GenePanelConfig attribute)

Y

Y_POSITIONS (pyhiv.report.constants.K03455Config attribute) (pyhiv.report.K03455Config attribute)

Y_SCALE (pyhiv.report.constants.GenePanelConfig attribute) (pyhiv.report.GenePanelConfig attribute)