TEcounter: a lightweight command-line tool for counting transposable elements from EDTA outputs

TEcounter is a lightweight Python command-line tool for counting transposable elements from EDTA output files. It is designed for transparent, reproducible TE quantification from EDTA annotations while preserving the distinction between GFF-derived annotation counts and EDTA copy-equivalent counts from companion summary files. The tool accepts EDTA GFF3 files, EDTA run prefixes, or directories containing a single EDTA GFF3 file. It can automatically discover companion *.out.fam.size.list, *.out.superfam.size.list, and *.tbl files, and produces a small, publication-ready output bundle including annotation tables, family and superfamily summaries, run-level summaries, and provenance metadata. TEcounter is intentionally narrow in scope. It does not attempt downstream comparative analysis or TE classification beyond EDTA’s own outputs. Instead, it focuses on robust counting, clear reporting, and explicit validation. When EDTA summary files are present, TEcounter checks family and superfamily summaries against one another and against RepeatMasker totals where available, helping users identify inconsistencies rather than silently masking them. The software is dependency-light, uses only the Python standard library, and is intended for scientists who need a simple, auditable, and reproducible way to summarise TE content from EDTA outputs.