7.1 Scope

Very similar to seq_query and mot_query, cla_query operation returns a list of cla names. It is designed for:

  • performing logical operations on lists of classifications
  • running full-text searches in the descriptions attached to every classification.

cla_query allows to search among classification entries exactly as seq_query does on seq entries, with the single difference that the constraint md5 does not exist1.

 

7.2 Out of Scope

  • If you want to use taxonomy to “filter” sequences, use hat_query (section 11).
  • For classifying motifs by taxonomy, use hot_query (section 12).

 

7.3 Options

The following constraints can be used in any combination and order. Please keep in mind that the constraints must be satisfied independantly (they are joined with a logical AND): if one of those is not fulfilled, the query will return an empty result.

cla_source=...
A non-empty list of classification database names.
cla_name=...
A list of classification entry names (given explicitly, or implicitly using query identifiers) to be included in the results.
and_cla_name=...
A list of classification entry names to be included in the results (logical AND with the previous constraint).
not_cla_name=...
A list of classification entry names to be excluded from the results (logical NOT to restrict the two previous constraints).
desc_text=...
A list of words to search for.
min_score=...
A positive real number.
prop_key=...
Limit the search to the sequence with the given property key(s).
prop_value=...
Limit the search to entries with the supplied property value(s). The exhaustive list of all entries matching the criteria is returned. This is a major distinction from the built-in synonymy mechanism that returns at most one sequence.
ancestor=...
A non-empty list of classification entry names or query identifiers that can return classification entries.
parent=...
A non-empty list of classification entry names or query identifiers that can return classification entries.
descendant=...
A non-empty list of classification entry names or query identifiers that can return classification entries.
child=...
A non-empty list of classification entry names or query identifiers that can return classification entries.
-lim=...
Maximum number of rows to be returned.
-ref=...
A query identifier, i.e. a string that starts with "$" followed by a letter, possibly followed by more letters, digits or underscores. This is how a query can be saved to be re-used later in other operations. When supplied, this option prevents the query to be executed.

1... just because a ’non-redundant part of the classification used for the computation’ does not exist.