generator

generator#

Generate simulated tandem repeat sequences from reference motifs.

This subcommand creates synthetic tandem repeat sequences by tiling one or more input motifs to a target length, optionally introducing random substitutions at a specified mutation rate. It is useful for benchmarking, testing downstream analysis pipelines, and generating controlled synthetic data.

Usage#

vampire generator -m <motif> ... -p <prefix> [options]

Examples#

# Generate a pure tandem repeat from a single motif
vampire generator -m GGC -l 1000 -r 0 -p output/prefix

# Generate a mixed tandem repeat from multiple motifs with 5% mutation
vampire generator -m GGC GGT -l 1000 -r 0.05 -p output/prefix

Options#

Option

Required

Default

Description

-m, --motifs

Yes

—

One or more reference motifs (e.g., GGC or GGC GGT)

-p, --prefix

Yes

—

Output prefix for generated files

-l, --length

No

1000

Total length of the simulated tandem repeat sequence (bp)

-r, --mutation-rate

No

0

Substitution mutation rate, between 0 and 1

-s, --seed

No

42

Random seed for reproducibility

--debug

No

False

Output debug information

Output Files#

Results are written with the provided <prefix>:

  • <prefix>.fa — Generated tandem repeat sequence

  • <prefix>.anno.tsv — mutation-aware motif annotation file

  • <prefix>.anno_woMut.tsv — motif annotation without mutation

Notes#

  • Motifs are tiled randomly to reach the target sequence length.

  • Mutations are applied uniformly across the entire sequence after tiling.

  • The output includes a FASTA file containing the generated sequence.

Contents