3  The GO OBITools library

3.1 BioSequence

The BioSequence class is used to represent biological sequences. It allows for storing : - the sequence itself as a []byte - the sequencing quality score as a []byte if needed - an identifier as a string - a definition as a string - a set of (key, value) pairs in a map[sting]interface{}

BioSequence is defined in the obiseq module and is included using the code

import (
    "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)

3.1.1 Creating new instances

To create new instance, use

• MakeBioSequence(id string, sequence []byte, definition string) obiseq.BioSequence
• NewBioSequence(id string, sequence []byte, definition string) *obiseq.BioSequence

Both create a BioSequence instance, but when the first one returns the instance, the second returns a pointer on the new instance. Two other functions MakeEmptyBioSequence, and NewEmptyBioSequence do the same job but provide an uninitialized objects.

• id parameters corresponds to the unique identifier of the sequence. It mist be a string constituted of a single word (not containing any space).
• sequence is the DNA sequence itself, provided as a byte array ([]byte).
• definition is a string, potentially empty, but usualy containing a sentence explaining what is that sequence.

import (
    "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)

func main() {
    myseq := obiseq.NewBiosequence(
        "seq_GH0001",
        bytes.FromString("ACGTGTCAGTCG"),
        "A short test sequence",
        )
}

When formated as fasta the parameters correspond to the following schema

>id definition containing potentially several words
sequence

3.1.2 End of life of a BioSequence instance

When a BioSequence instance is no more used, it is normally taken in charge by the GO garbage collector. You can if you want call the Recycle method on the instance to store the allocated memory element in a pool to limit allocation effort when many sequences are manipulated.

3.1.3 Accessing to the elements of a sequence

The different elements of an obiseq.BioSequence must be accessed using a set of methods. For the three main elements provided during the creation of a new instance methodes are :

• Id() string
• Sequence() []byte
• Definition() string

It exists pending method to change the value of these elements

• SetId(id string)
• SetSequence(sequence []byte)
• SetDefinition(definition string)

import (
    "fmt"
    "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)

func main() {
    myseq := obiseq.NewBiosequence(
        "seq_GH0001",
        bytes.FromString("ACGTGTCAGTCG"),
        "A short test sequence",
        )

    fmt.Println(myseq.Id())
    myseq.SetId("SPE01_0001")
    fmt.Println(myseq.Id())
}

3.1.3.1 Different ways for accessing an editing the sequence

If Sequence()and SetSequence(sequence []byte) methods are the basic ones, several other methods exist.

• String() string return the sequence directly converted to a string instance.
• The Write method family allows for extending an existing sequence following the buffer protocol.
  • Write(data []byte) (int, error) allows for appending a byte array on 3’ end of the sequence.
  • WriteString(data string) (int, error) allows for appending a string.
  • WriteByte(data byte) error allows for appending a single byte.

The Clear method empties the sequence buffer.

import (
    "fmt"
    "git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)

func main() {
    myseq := obiseq.NewEmptyBiosequence()

    myseq.WriteString("accc")
    myseq.WriteByte(byte('c'))
    fmt.Println(myseq.String())
}

3.1.3.2 Sequence quality scores

Sequence quality scores cannot be initialized at the time of instance creation. You must use dedicated methods to add quality scores to a sequence.

To be coherent the length of both the DNA sequence and que quality score sequence must be equal. But assessment of this constraint is realized. It is of the programmer responsability to check that invariant.

While accessing to the quality scores relies on the method Quality() []byte, setting the quality need to call one of the following method. They run similarly to their sequence dedicated conterpart.

• SetQualities(qualities Quality)
• WriteQualities(data []byte) (int, error)
• WriteByteQualities(data byte) error

In a way analogous to the Clear method, ClearQualities() empties the sequence of quality scores.