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` #

The qualities method extracts or sets the quality scores of a BioSequence object. When used with no parameter, it returns a table containing the quality values.

sequence = BioSequence.new("seq_id", "gctagctg", "@@@FFFFHHH")
qualities = sequence:qualities()
for _, q in ipairs(qualities) do
    print(q)
end

A quality score table can be provided to the qualities method to update the quality scores of the BioSequence object.

sequence = BioSequence.new("seq_id", "gctagctg")
sequence:qualities({65, 66, 67, 68, 69, 70, 71, 72})
qualities = sequence:qualities()
for _, q in ipairs(qualities) do
    print(q)
end

`definition` #

The definition method extracts or sets the sequence definition of a BioSequence object. When used with no parameter, it returns a string or nil if no definition is set.

sequence = BioSequence.new("seq_id", "gctagctg", "This is a test sequence")
print(sequence:definition())

A string parameter representing the sequence definition can be provided to the definition method to update the definition of the BioSequence object.

sequence = BioSequence.new("seq_id", "gctagctg")
sequence:definition("New definition for the sequence")
print(sequence:definition())

`count` #

The count method extracts or sets the count value from a BioSequence object. When used with no parameter, it returns a number or 1 if no count is set.

sequence = BioSequence.new("seq_id", "gctagctg")
print(sequence:count())

A number parameter representing the count can be provided to the count method to update the count of the BioSequence object.

sequence = BioSequence.new("seq_id", "gctagctg")
sequence:count(10)
print(sequence:count())

`taxid` #

The taxid method extracts or sets the taxonomical identifier from a BioSequence object. When used with no parameter, it returns a string or nil if no taxid is set.

sequence = BioSequence.new("seq_id", "gctagctg")
print(sequence:taxid())

A string parameter representing the taxid can be provided to the taxid method to update the taxonomical identifier of the BioSequence object.

sequence = BioSequence.new("seq_id", "gctagctg")
sequence:taxid("9606")
print(sequence:taxid())

`taxon` #

The taxon method extracts the taxonomical information from a BioSequence object. When used with no parameter, it returns a Taxon object or nil if no taxonomic data is associated with the sequence.

sequence = BioSequence.new("seq_id", "gctagctg")
taxon = sequence:taxon()
if taxon then
    print(taxon:name())
end

A Taxon parameter can be provided to the taxon method to update the taxonomic information of the BioSequence object.

sequence = BioSequence.new("seq_id", "gctagctg")
taxon = Taxon.new("Homo sapiens", "9606")
sequence:taxon(taxon)
taxon = sequence:taxon()
if taxon then
    print(taxon:name())
end

`attribute` #

The attribute method extracts or sets an attribute value of a BioSequence object. When used with one parameter (the attribute name), it returns the attribute value or nil if the attribute does not exist.

sequence = BioSequence.new("seq_id", "gctagctg")
print(sequence:attribute("custom"))

A value can be provided as a third parameter to set an attribute on the BioSequence object.

sequence = BioSequence.new("seq_id", "gctagctg")
sequence:attribute("custom", "value")
print(sequence:attribute("custom"))

`len` #

The len method returns the length of the nucleic sequence as a number.

sequence = BioSequence.new("seq_id", "gctagctg")
print(sequence:len())

`has_sequence` #

The has_sequence method checks if the BioSequence object contains a nucleic sequence. It returns a boolean value (true or false).

sequence = BioSequence.new("seq_id", "gctagctg")
print(sequence:has_sequence())

`has_qualities` #

The has_qualities method checks if the BioSequence object contains quality scores. It returns a boolean value (true or false).

sequence = BioSequence.new("seq_id", "gctagctg", "@@@FFFF")
print(sequence:has_qualities())

`source` #

The source method extracts or sets the source information from a BioSequence object. It returns a string or nil if no source is set.

sequence = BioSequence.new("seq_id", "gctagctg")
sequence:source("source_file.fasta")
print(sequence:source())

`md5` #

The md5 method computes the MD5 hash of the sequence and returns it as a table of 16 integers representing the hash bytes.

sequence = BioSequence.new("seq_id", "gctagctg")
md5_table = sequence:md5()
for i, byte_val in ipairs(md5_table) do
    print(byte_val)
end

`md5_string` #

The md5_string method computes the MD5 hash of the sequence and returns it as a hexadecimal string.

sequence = BioSequence.new("seq_id", "gctagctg")
md5_str = sequence:md5_string()
print(md5_str)

`subsequence` #

The subsequence method extracts a subsequence from the BioSequence object. It accepts two parameters: start and end positions (1-indexed inclusive). It returns a new BioSequence object containing the subsequence.

sequence = BioSequence.new("seq_id", "gctagctgtgatgctgatgctagct")
subseq = sequence:subsequence(5, 10)
print(subseq:id())
print(subseq:sequence())

`reverse_complement` #

The reverse_complement method computes and returns the reverse complement of the nucleic sequence as a new BioSequence object.

sequence = BioSequence.new("seq_id", "gctagctg")
revcomp = sequence:reverse_complement()
print(revcomp:sequence())

`fasta` #

The fasta method converts the BioSequence object to FASTA format string. It accepts an optional format parameter (“json” or “obi”) to specify the header format. Default format is JSON header.

sequence = BioSequence.new("seq_id", "gctagctg", "Test sequence")
fasta_str = sequence:fasta("json")
print(fasta_str)

sequence = BioSequence.new("seq_id", "gctagctg", "Test sequence")
fasta_str = sequence:fasta("obi")
print(fasta_str)

`fastq` #

The fastq method converts the BioSequence object to FASTQ format string. It accepts an optional format parameter (“json” or “obi”) to specify the header format. Default format is JSON header.

sequence = BioSequence.new("seq_id", "gctagctg", "Test sequence", {65, 66, 67, 68, 69, 70, 71, 72})
fastq_str = sequence:fastq("json")
print(fastq_str)

`string` #

The string method returns a string representation of the BioSequence object. The format depends on whether the sequence has quality scores: FASTQ format if qualities are present, FASTA format otherwise. It accepts an optional format parameter (“json” or “obi”) to specify the header format.

sequence = BioSequence.new("seq_id", "gctagctg", "Test sequence")
seq_str = sequence:string("obi")
print(seq_str)

The BioSequence class #

Constructor of BioSequence #

BioSequence Methods #

id : the sequence identifier #

sequence : the nucleic sequence #

qualities #

definition #

count #

taxid #

taxon #

attribute #

len #

has_sequence #

has_qualities #

source #

md5 #

md5_string #

subsequence #

reverse_complement #

fasta #

fastq #

string #