Default genome fasta location resolver
Default genome fasta location resolver
(get-params & ks)
Returns the value(s) indexed by ks. ks is either a single keyword, an enumeration of keywords, or a vector of keywords. The single keyword returns the top level params db value indexed by the keyword. An enumerated listing of keywords returns all top level params db values indexed by each keyword. A vector of keywords returns the multi-level value associated with the keyword path in the params db (like get-in).
Returns the value(s) indexed by ks. ks is either a single keyword, an enumeration of keywords, or a vector of keywords. The single keyword returns the top level params db value indexed by the keyword. An enumerated listing of keywords returns all top level params db values indexed by each keyword. A vector of keywords returns the multi-level value associated with the keyword path in the params db (like get-in).
(param-ks)
Returns the set of keys indexing the params db. Only the first level
Returns the set of keys indexing the params db. Only the first level
(param-set)
(set-configuration config-map)
Sets up the params db and sets the default values for genome fasta dir and blast database. The basic shape of the config-map requires a :genomes submap and a :blast submap. Each of these requires a :default field and the value of the default field should be a keyword indexing the containing map (genomes/blast) and its value will be this indexed value.
The config-map is presumed to have been obtained by reading a configuration map in a config file. For example, as by:
(->> config-file-spec slurp clojure.tools.reader.edn/read-string)
Sets up the params db and sets the default values for genome fasta dir and blast database. The basic shape of the config-map requires a :genomes submap and a :blast submap. Each of these requires a :default field and the value of the default field should be a keyword indexing the containing map (genomes/blast) and its value will be this indexed value. The config-map is presumed to have been obtained by reading a configuration map in a config file. For example, as by: (->> config-file-spec slurp clojure.tools.reader.edn/read-string)
(with-blast-db dbref & body)
Binds DBREF as the current blast database. DBREF is a blast database specification as expected by NCBI blast cmds. Executes BODY (a group of forms) within context so bound - including across threads
Binds DBREF as the current blast database. DBREF is a blast database specification as expected by NCBI blast cmds. Executes BODY (a group of forms) within context so bound - including across threads
(with-genome-db dbref & body)
Binds DBREF as the current genome fasta directory resolver. DBREF is a genome db fasta directory resolver, which is a function of 1 argument returning the director for the genome name passed in. Executes BODY (a group of forms) within context so bound - including across threads
Binds DBREF as the current genome fasta directory resolver. DBREF is a genome db fasta directory resolver, which is a function of 1 argument returning the director for the genome name passed in. Executes BODY (a group of forms) within context so bound - including across threads
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