mTRplotter

mTRplotter turns the read-length plotting logic from the notebook into a small Python CLI.

Each run also writes params.json and log.out alongside the figure and TSV outputs so the command parameters and progress logs stay with the generated results.

Installation

pip install mtrplotter

It expects a tab-delimited sample table with at least:

• sample
• medaka_folder
• software (medaka or trgt)
• flank_bp
• any number of extra metadata columns

If --output-dir is omitted, mTRplotter writes all outputs to the current working directory.

For each requested locus, it:

• validates medaka rows against each sample's ref_chunks.fasta
• validates TRGT rows against each sample's .trgt.vcf.gz
• extracts medaka reads from trimmed_reads_to_poa.bam through the BAM index
• extracts TRGT reads from .trgt.spanning.bam
• extracts read lengths for the requested locus or BED subset
• writes per-read and summary tables
• produces one figure per locus with samples on the x-axis and trimmed read length on the y-axis

Usage

Single locus:

python -m mtrplotter \
  --sample-table examples/samples.tsv \
  --region chr1:99682978-99683197 \
  --label-columns tissue_name tech core technology \
  --jobs 10

BED input:

python -m mtrplotter \
  --sample-table samples.tsv \
  --bed regions.bed \
  --output-dir results \
  --catalog-bed catalog.bed

If --catalog-bed is not provided, loci are still checked against each sample's ref_chunks.fasta, which reflects the regions actually used by the medaka run.

Metadata should already be present in the sample table. There is no separate manifest join step at runtime.

The bundled example table keeps inline columns such as tissue, tissue_name, tech, core, and technology so plotting labels can be chosen directly from the sample table.

For medaka rows, the plotted length is raw_length - 2 * flank_bp, where flank_bp comes from the sample table.

For TRGT rows, the software looks for the FL BAM tag and uses raw_length - left_flank - right_flank. If the FL tag is absent, it falls back to the sample-table flank_bp.

For TRGT rows, use the medaka_folder column as a generic input path. The most reliable form is a per-sample TRGT prefix such as:

sample	medaka_folder	software	flank_bp
SAMPLE001	/path/to/trgt/SAMPLE001	trgt	50

mTRplotter resolves the sibling files:

• .trgt.vcf.gz
• .trgt.spanning.bam