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BenchBaze - DNA Annotation Module

This DNA map annotation tool based on pLannotate, adapted for, and integrated in, BenchBaze.

It provides functions to annotate DNA sequences and export the results in BenchBaze.

Setup

  1. Create and activate an environment.
conda env create -f environment.yml
conda activate plannotate
  1. Install the package.
python setup.py install
  1. Download the annotation databases (required).
python -c "from plannotate import resources; resources.download_databases()"

Usage

Use the module directly from Python:

from plannotate.annotate import annotate
from plannotate import resources

seq = "ATGCGT..."  # input DNA sequence

# Detailed annotation dataframe
hits = annotate(seq, is_detailed=True, linear=False)

# Export GenBank text
gbk_text = resources.get_gbk(hits, seq)

# Export Biopython SeqRecord
seq_record = resources.get_seq_record(hits, seq)

# Export cleaned report dataframe
csv_df = resources.get_clean_csv_df(hits)

BenchBaze Integration

  • accept uploaded sequence/plasmid data in BenchBaze
  • call annotate(...) in your service layer
  • store or return get_clean_csv_df(...) output for UI/reporting
  • optionally generate GenBank output with get_gbk(...)

Notes

  • External binaries must be available on PATH: blastn, diamond, cmscan, rg.

Credits

pLannotate was originally developed by Matthew J McGuffie in the Barrick Lab at The University of Texas at Austin, https://doi.org/10.1093/nar/gkab374.