Difference between revisions of "Genome derivative files"
From CoGepedia
(Created page with '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 load...') |
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* /storage/coge/data/bed/ | * /storage/coge/data/bed/ | ||
| − | * /storage/coge/data/blast/ | + | ** file format: genom_id.bed |
| − | * /storage/coge/data/last/ | + | |
| + | * /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/ | * /storage/coge/data/cache/ | ||
| + | ** subdirectory with genome_id needs to be deleted | ||
| + | |||
* /storage/coge/data/fasta/ | * /storage/coge/data/fasta/ | ||
| + | ** files are created with genome_id as the predicate | ||
| + | ** need to delete: genome_id* | ||
| + | |||
* /storage/coge/diags/ | * /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 | ||
Revision as of 10:19, 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: genom_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
