{"__v":0,"_id":"57619493aa540f3600bfed51","category":{"__v":0,"_id":"57619455a7c9f729009a74e0","project":"57618347b65324200072d6a5","version":"57618347b65324200072d6a8","sync":{"url":"","isSync":false},"reference":false,"createdAt":"2016-06-15T17:45:57.617Z","from_sync":false,"order":5,"slug":"file-descriptions","title":"File formats"},"parentDoc":null,"project":"57618347b65324200072d6a5","user":"57617c8caa540f3600bfed20","version":{"__v":8,"_id":"57618347b65324200072d6a8","project":"57618347b65324200072d6a5","createdAt":"2016-06-15T16:33:11.587Z","releaseDate":"2016-06-15T16:33:11.587Z","categories":["57618347b65324200072d6a9","5761912d207db7170022fbe9","57619455a7c9f729009a74e0","576e8ae1f37ab41700147471","5797b8e5209a6e0e00b8321b","57989a8817ced017003c4c69","579ca6f3d46f960e0029a8ec","579ca703fefb1d0e00c94f06"],"is_deprecated":false,"is_hidden":false,"is_beta":false,"is_stable":true,"codename":"blobtools v0.9.19","version_clean":"0.9.19","version":"0.9.19"},"updates":[],"next":{"pages":[],"description":""},"createdAt":"2016-06-15T17:46:59.553Z","link_external":false,"link_url":"","githubsync":"","sync_unique":"","hidden":false,"api":{"results":{"codes":[]},"settings":"","auth":"required","params":[],"url":""},"isReference":false,"order":3,"body":"## Why is it needed?\n\n* During the [taxonomic annotation](doc:taxonomic-annotation) process, ```blobtools``` uses a [nodesDB file](doc:taxonomy-database) to infer the [taxonomy](doc:taxonomy) at each [rank](doc:taxonomic-rank) for each of the hits in a [hits file](doc:taxonomy-file) based on the [taxID](doc:taxid) of the hit\n\n\n* A [nodesDB file](doc:taxonomy-database) is a \"condensed\" version of NCBI's ```nodes.dmp``` and ```names.dmp``` files and faster to parse\n\n## Required format\n* A header indicating the number of nodes, followed by TAB-separated lines containing\n * taxID of node\n * taxonomic rank of node\n * name of node\n * taxID of parent node\n\n# Generating a nodesDB file\n\n\n* a file named ```nodesDB.txt``` is created in the folder ```blobtools/data/``` when ```blobtools``` is provided with NCBI's ```names.dmp``` and ```nodes.dmp``` using the ```[--names]``` and ```[--nodes]``` arguments\n\n\n* the commands for doing this are listed in the [installation](doc:getting-started#installation) section","excerpt":"","slug":"taxonomy-database","type":"basic","title":"nodesDB file"}
## Why is it needed? * During the [taxonomic annotation](doc:taxonomic-annotation) process, ```blobtools``` uses a [nodesDB file](doc:taxonomy-database) to infer the [taxonomy](doc:taxonomy) at each [rank](doc:taxonomic-rank) for each of the hits in a [hits file](doc:taxonomy-file) based on the [taxID](doc:taxid) of the hit * A [nodesDB file](doc:taxonomy-database) is a "condensed" version of NCBI's ```nodes.dmp``` and ```names.dmp``` files and faster to parse ## Required format * A header indicating the number of nodes, followed by TAB-separated lines containing * taxID of node * taxonomic rank of node * name of node * taxID of parent node # Generating a nodesDB file * a file named ```nodesDB.txt``` is created in the folder ```blobtools/data/``` when ```blobtools``` is provided with NCBI's ```names.dmp``` and ```nodes.dmp``` using the ```[--names]``` and ```[--nodes]``` arguments * the commands for doing this are listed in the [installation](doc:getting-started#installation) section