Genome derivative files

CoGe generates several derivative files for a genome. These are used in various analyses including blast, synmap, etc. If a genome has been modified (e.g., bad annotations loaded), these derivative files need to be deleted.

• /storage/coge/data/bed/
  • file format: genome_id.bed

• /storage/coge/data/blast/db/
  • subdirectory with genome_id needs to be deleted
  • Note: Currently an inconsistency where blastdb files are being deposited in the main directory and not a subdirectory

• /storage/coge/data/last/db/
  • subdirectory with genome_id needs to be deleted
  • Note: Currently an inconsistency where blastdb files are being deposited in the main directory and not a subdirectory

• /storage/coge/data/cache/
  • subdirectory with genome_id needs to be deleted

• /storage/coge/data/fasta/
  • files are created with genome_id as the predicate
  • need to delete: genome_id-*

• /storage/coge/diags/
  • data are storage in subdirectories: /genome_id_1/genome_id_2/
  • All directories need to be crawled to find cases where genome_id_2 exists
  • Entire contents of directory need to be deleted

There is a script to generate the delete commands: ./scripts/delete_genome_derivative_files.pl