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aerial.bio.utils.params


default-blast-dbclj

Default blast database

Default blast database
raw docstring

default-genome-fasta-dirclj

Default genome fasta location resolver

Default genome fasta location resolver
raw docstring

get-paramsclj

(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).
raw docstring

param-ksclj

(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
raw docstring

param-setclj

(param-set)

paramsclj


set-configurationclj

(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)
raw docstring

with-blast-dbcljmacro

(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
raw docstring

with-genome-dbcljmacro

(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
raw docstring

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