mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
98 lines
3.0 KiB
Plaintext
98 lines
3.0 KiB
Plaintext
# 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](https://pkg.go.dev/github.com/PaesslerAG/gval "Gval (Go eVALuate) for evaluating arbitrary expressions Go-like expressions.") go package, which allows for evaluating go-Like expression.
|
|
|
|
## Variables usable in the expression
|
|
|
|
- `sequence` is the sequence object on which the expression is evaluated.
|
|
- `annotations`is a map object containing every annotations associated to the currently processed sequence.
|
|
|
|
## Function defined in the language
|
|
|
|
### Instrospection functions {.unnumbered}
|
|
|
|
**`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`.
|
|
|
|
### Cast functions {.unnumbered}
|
|
|
|
**`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 {.unnumbered}
|
|
|
|
**`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 {.unnumbered}
|
|
|
|
**`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`.
|
|
|
|
### 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.
|
|
|
|
$$
|
|
Skew_{GC}=\frac{G-C}{G+C}
|
|
$$
|
|
|
|
## 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.
|
|
|
|
```go
|
|
annotations["direction"]
|
|
```
|
|
|
|
The above code retreives the `direction` annotation. A second notation using the dot (`.`) is often
|
|
more convenient.
|
|
|
|
```go
|
|
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()`
|
|
|
|
```go
|
|
sequence.Id()
|
|
```
|
|
|