7  OBITools expression language

Several OBITools (e.g. obigrep, obiannotate) allow the user to specify some simple expressions to compute values or define predicates. This expressions are parsed and evaluated using the gval go package, which allows for evaluating go-Like expression.

7.1 Variables usable in the expression

• sequence is the sequence object on which the expression is evaluated.
• annotationsis a map object containing every annotations associated to the currently processed sequence.

7.2 Function defined in the language

Instrospection functions

len(x)

It is a generic function allowing to retreive the size of a object. It returns the length of a sequences, the number of element in a map like annotations, the number of elements in an array. The reurned value is an int.

contains(map,key)

Tests if the map contains a value assciated to key

Cast functions

int(x)

Converts if possible the x value to an integer value. The function returns an int.

numeric(x)

Converts if possible the x value to a float value. The function returns a float.

bool(x)

Converts if possible the x value to a boolean value. The function returns a bool.

String related functions

printf(format,...)

Allows to combine several values to build a string. format follows the classical C printf syntax. The function returns a string.

subspc(x)

substitutes every space in the x string by the underscore (_) character. The function returns a string.

Condition function

ifelse(condition,val1,val2)

The condition value has to be a bool value. If it is true the function returns val1, otherwise, it is returning val2.

7.2.1 Sequence analysis related function

composition(sequence)

The nucleotide composition of the sequence is returned as as map indexed by a, c, g, or t and each value is the number of occurrences of that nucleotide. A fifth key others accounts for all others symboles.

gcskew(sequence)

Computes the excess of g compare to c of the sequence, known as the GC skew.

\[ Skew_{GC}=\frac{G-C}{G+C} \]

7.3 Accessing to the sequence annotations

The annotations variable is a map object containing all the annotations associated to the currently processed sequence. Index of the map are the attribute names. It exists to possibillities to retreive an annotation. It is possible to use the classical [] indexing operator, putting the attribute name quoted by double quotes between them.

annotations["direction"]

The above code retreives the direction annotation. A second notation using the dot (.) is often more convenient.

annotations.direction

Special attributes of the sequence are accessible only by dedicated methods of the sequence object.

• The sequence identifier : Id()
• THe sequence definition : Definition()

sequence.Id()