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Minimal test dataset

This minimal dataset verifies that ORFannotate is installed and functioning correctly. It runs on a small, realistic subset of the genome and completes in just a few seconds using minimal memory.

Included files

  • toy.gtf – a minimal GTF file with a few transcripts and exons.
  • toy.fa – a matching reference FASTA containing only the sequences required by toy.gtf.

Running this test takes only a few seconds and completes the full ORFannotate workflow, including sequence reconstruction, ORF prediction, CDS annotation, and summary table generation.

Test command

conda activate ORFannotate

python ORFannotate.py \
  --gtf tests/test_data/toy.gtf \
  --fa tests/test_data/toy.fa \
  --species human \
  --outdir output/

This will create:

  • output/transcripts.fa – reconstructed transcript sequences.
  • output/CPAT/ – CPAT results.
  • output/ORFannotate_annotated.gtf – GTF with CDS features inserted.
  • output/ORFannotate_summary.tsv – transcript-level summary table.
  • output/ORFannotate.log – run log.