The BioSequence class #

The BioSequence class corresponds to the OBITools representation of a nucleic sequence.

Constructor of BioSequence #

The BioSequence constructor accepts three parameters:

• sequence_id: a string corresponding to the sequence id. The sequence id cannot contain white character.
• dna_sequence: a string representing a nucleic sequence. The string is converted to lowercases and must only contain characters corresponding to IUPAC code.
• definition: this parameter is optional. If present, it corresponds to an unstructured text, used to describe the sequence.

sequence = BioSequence.new("sequence_id","gctagctgtgatgctgatgctagct")

BioSequence Methods #

id : the sequence identifier #

Extract the sequence identifier from a BioSequence object. The method doesn’t accept any parameter and returns a string.

sequence = BioSequence.new("sequence_id","gctagctgtgatgctgatgctagct")
print(sequence:id())

sequence_id

A string parameter representing a nucleic sequence can be provided to the id method. In this case, the id of the BioSequence object is substituted by the new string. The method does not return anything.

sequence = BioSequence.new("sequence_id","gctagctgtgatgctgatgctagct")
print(sequence:id())
sequence:sequence("new_id")
print(sequence:id())

sequence_id
new_id

sequence : the nucleic sequence #

When used with no parameter, the method extracts the nucleic sequence itself from the BioSequence object. In this condition, it returns a string.

sequence = BioSequence.new("sequence_id","gctagctgtgatgctgatgctagct")
print(sequence:sequence())

gctagctgtgatgctgatgctagct

A string parameter representing a nucleic sequence can be provided to the sequence method. In this case, the current sequence of the object is substituted by the new string. The method does not return anything.

sequence = BioSequence.new("sequence_id","gctagctgtgatgctgatgctagct")
print(sequence:sequence())
sequence:sequence("cgatctagcta")
print(sequence:sequence())

gctagctgtgatgctgatgctagct
cgatctagcta

qualities #

definition #

count #

taxid #

taxon #

attribute #

len #

has_sequence #

has_qualities #

source #

md5 #

md5_string #

subsequence #

reverse_complement #

fasta #

fastq #

string #