"""
PDF report generation for PyHIV results.
"""
import textwrap
from typing import Dict, List, Optional, Tuple
import matplotlib.pyplot as plt
from matplotlib.backends.backend_pdf import PdfPages
from matplotlib.gridspec import GridSpec
from .constants import PageLayout, MetadataConfig
from .utils import ungap, first_last_nongap_idx
from .visualization import plot_gene_axes
[docs]
def render_sequence_page(
pdf: PdfPages,
sequence: str,
accession: str,
subtype: str,
mm_region: str,
present_regions: List[str],
features_aln: Dict[str, Tuple[int, int]],
ref_seq_aligned: str,
user_seq_aligned: str,
y_positions: Optional[Dict[str, float]] = None
):
"""
Render a single sequence page in the PDF report.
Parameters
----------
pdf : PdfPages
The PdfPages object to save the figure into.
sequence : str
The name or identifier of the sequence.
accession : str
The accession number of the sequence.
subtype : str
The subtype of the sequence.
mm_region : str
The most matching region of the sequence.
present_regions : List[str]
List of present regions in the sequence.
features_aln : Dict[str, Tuple[int, int]]
Dictionary of gene features with their alignment coordinate ranges.
ref_seq_aligned : str
The reference sequence aligned (with gaps).
user_seq_aligned : str
The user's sequence aligned (with gaps).
y_positions : Optional[Dict[str, float]], optional
Fixed y-positions for gene lanes, by default None (auto lanes).
"""
fig = plt.figure(figsize=PageLayout.FIGSIZE)
gs = GridSpec(
2, 1, # one column
height_ratios=PageLayout.GRID_HEIGHT_RATIOS,
figure=fig,
hspace=PageLayout.HSPACE
)
# Top: metadata (wrapped) — no bar chart
ax_meta = fig.add_subplot(gs[0, 0])
ax_meta.axis("off")
ax_meta.text(0.5, MetadataConfig.TITLE_Y, f"PyHIV Report — {sequence}", ha="center", va="top",
fontsize=16, fontweight="bold", transform=ax_meta.transAxes)
ref_len_nt = len(ungap(ref_seq_aligned))
usr_len_nt = len(ungap(user_seq_aligned))
meta_lines = [
f"Sequence: {sequence}",
f"Subtype: {subtype}",
f"Reference Accession: {accession}",
f"Most matching region: {mm_region or '-'}",
f"Present regions ({len(present_regions)}): {', '.join(present_regions) if present_regions else '-'}",
f"Lengths — nt (no gaps) Ref|Seq: {ref_len_nt} | {usr_len_nt}",
]
wrapped = "\n".join(textwrap.fill(l, width=MetadataConfig.WRAP, subsequent_indent=' ') for l in meta_lines)
ax_meta.text(0.0, MetadataConfig.INFO_TOP_Y, wrapped, ha="left", va="top",
family="monospace", fontsize=MetadataConfig.FONTSIZE, transform=ax_meta.transAxes, wrap=True)
# Bottom: gene panel (full width)
ax_map = fig.add_subplot(gs[1, 0])
a_start, a_end = first_last_nongap_idx(user_seq_aligned)
plot_gene_axes(
ax=ax_map,
genes_ranges=features_aln,
alignment_start=a_start,
alignment_end=a_end,
y_positions=y_positions,
)
pdf.savefig(fig)
plt.close(fig)