Genome derivative files: Difference between revisions
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* /storage/coge/data/fasta/ | * /storage/coge/data/fasta/ | ||
** files are created with genome_id as the predicate | ** files are created with genome_id as the predicate | ||
** need to delete: genome_id* | ** need to delete: genome_id-* | ||
* /storage/coge/diags/ | * /storage/coge/diags/ | ||
| Line 23: | Line 23: | ||
** All directories need to be crawled to find cases where genome_id_2 exists | ** All directories need to be crawled to find cases where genome_id_2 exists | ||
** Entire contents of directory need to be deleted | ** Entire contents of directory need to be deleted | ||
There is a script to generate the delete commands: ./scripts/delete_genome_derivative_files.pl | |||
Latest revision as of 18:09, 22 July 2014
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