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Report generation

Teloscope can generate a PDF report during a FASTA run:

teloscope asm.fa -o results/ -r -e -g -i --plot-report

This writes results/asm.fa_plot_report.pdf.

-r is recommended with --plot-report so the report includes repeat-density, canonical-ratio, and strand-bias tracks. GC and entropy tracks are added automatically when their files are present.

Assembly record filters apply before these files are written. This example uses exact chromosome accession.version IDs derived from assembly metadata and omits every other record from the TSV, BED/BEDgraph files, and PDF:

teloscope asm.fa -o results/ --include-bed chromosomes.ids -r --plot-report

Prefix filters are also available, but database prefixes are not universal chromosome labels. Inspect the FASTA primary IDs before using --include-prefix.

What the report contains

  • page 1: assembly overview, scaffold classes, and flagged scaffolds
  • page 2: telomere length summary and flagged telomere blocks
  • later pages: one terminal zoom figure per scaffold with called telomere blocks

Each terminal zoom page can include:

  • telomere block positions
  • gap intervals
  • repeat density
  • canonical ratio
  • strand bias
  • GC content
  • entropy

Standalone plotting

The plotting script can be run on an existing Teloscope output directory:

python3 scripts/teloscope_report.py results/ -o report.pdf
python3 scripts/teloscope_report.py results/ --png -o figures/

The script auto-detects the Teloscope files in that directory.

For a single interstitial telomeric sequence locus, use plot_its.py on the same output directory:

python3 scripts/plot_its.py results/ CHROM:START-END -o its.pdf
python3 scripts/plot_its.py results/ CHROM --png -o its_figures/

A bare CHROM auto-centers on the largest interstitial telomere cluster on that scaffold.

Minimum required input:

  • *_terminal_telomeres.bed

Common optional inputs:

  • *_gaps.bed
  • *_window_repeat_density.bedgraph
  • *_window_canonical_ratio.bedgraph
  • *_window_strand_ratio.bedgraph
  • *_window_gc.bedgraph
  • *_window_entropy.bedgraph
  • *_report.tsv

Standalone script options

Flag Meaning Default
-o output file for PDF mode or output directory for PNG mode <input_dir>/teloscope_report.pdf
--png write one PNG per page instead of one PDF false
--dpi raster DPI 450
--draft use 150 DPI for fast iteration false

Requirements

  • Python 3
  • matplotlib
  • numpy
  • pandas

Regression check

The report layout regression script lives in scripts/:

python3 scripts/test_teloscope_report.py

It checks the plotting code directly and does not need a full Teloscope run on disk.