/detect_plasmid

Primary LanguagePythonMIT LicenseMIT

detect_plasmid

An example preparation workflow is presented in refseq_prepare.sh

Workflow:

  1. refseq_cds_extractor.py - extract the nucleotide coding sequences and taxonomy
  2. refseq_cds_filter.py - filter the extracted cds file by minimum sequence length
  3. refseq_cds_balance.py - concatenate the matched and not matched taxa files and balance the number of sequences in each class
  4. refseq_cds_savemat.py - format the coding sequences tagged by taxa class and save into a .mat file for use with PyTorch, also partitions train, validation and test