class Seq
# Quality scores bases
- SCORE_BASE = 64
+ SCORE_BASE = 33
SCORE_MIN = 0
SCORE_MAX = 40
def self.new_bp(record)
seq_name = record[:SEQ_NAME]
seq = record[:SEQ]
- type = record[:SEQ_TYPE]
+ type = record[:SEQ_TYPE].to_sym if record[:SEQ_TYPE]
qual = record[:SCORES]
self.new(seq_name, seq, type, qual)
raise SeqError, "Cannot generate negative oligo length: #{length}" if length <= 0
case type.downcase
- when /dna/ then alph = DNA
- when /rna/ then alph = RNA
- when /protein/ then alph = PROTEIN
+ when :dna then alph = DNA
+ when :rna then alph = RNA
+ when :protein then alph = PROTEIN
else
raise SeqError, "Unknown sequence type: #{type}"
end
raise SeqError, "Guess failed: sequence is nil" if self.seq.nil?
case self.seq[0 ... 100].downcase
- when /[flpqie]/ then return "protein"
- when /[u]/ then return "rna"
- else return "dna"
+ when /[flpqie]/ then return :protein
+ when /[u]/ then return :rna
+ else return :dna
end
end
# Method that returns true is a given sequence type is DNA.
def is_dna?
- self.type == 'dna'
+ self.type == :dna
end
# Method that returns true is a given sequence type is RNA.
def is_rna?
- self.type == 'rna'
+ self.type == :rna
end
# Method that returns true is a given sequence type is protein.
def is_protein?
- self.type == 'protein'
+ self.type == :protein
end
# Method to transcribe DNA to RNA.
def to_rna
raise SeqError, "Cannot transcribe 0 length sequence" if self.length == 0
raise SeqError, "Cannot transcribe sequence type: #{self.type}" unless self.is_dna?
- self.type = 'rna'
+ self.type = :rna
self.seq.tr!('Tt','Uu')
end
def to_dna
raise SeqError, "Cannot reverse-transcribe 0 length sequence" if self.length == 0
raise SeqError, "Cannot reverse-transcribe sequence type: #{self.type}" unless self.is_rna?
-
- self.type = 'dna'
+ self.type = :dna
self.seq.tr!('Uu','Tt')
end
# Method to translate a DNA sequence to protein.
def translate!(trans_tab = 11)
- raise SeqError, "Sequence type must be 'dna' - not #{self.type}" unless self.type == 'dna'
+ raise SeqError, "Sequence type must be 'dna' - not #{self.type}" unless self.type == :dna
raise SeqError, "Sequence length must be a multiplum of 3 - was: #{self.length}" unless (self.length % 3) == 0
case trans_tab
self.seq = protein
self.qual = nil
- self.type = "protein"
+ self.type = :protein
self
end
def generate(length, type)
raise SeqError, "Cannot generate sequence length < 1: #{length}" if length <= 0
- case type.downcase
- when "dna"
- alph = DNA
- when "rna"
- alph = RNA
- when "protein"
- alph = PROTEIN
+ case type
+ when :dna then alph = DNA
+ when :rna then alph = RNA
+ when :protein then alph = PROTEIN
else
raise SeqError, "Unknown sequence type: #{type}"
end
seq_new = Array.new(length) { alph[rand(alph.size)] }.join("")
self.seq = seq_new
- self.type = type.downcase
+ self.type = type
seq_new
end
self
end
+ # Method to concatenate sequence entries.
+ def <<(entry)
+ raise SeqError, "sequences of different types" unless self.type == entry.type
+ raise SeqError, "qual is missing in one entry" unless self.qual.class == entry.qual.class
+
+ self.seq << entry.seq
+ self.qual << entry.qual unless entry.qual.nil?
+
+ self
+ end
+
# Method that returns a subsequence of from a given start position
# and of a given length.
def subseq(start, length = self.length - start)
def qual_base33?
self.qual.match(/[!-:]/) ? true : false
end
-
- # Method that determines if a quality score string can be
- # absolutely identified as base 64.
+
+ # Method that determines if a quality score string may be base 64.
def qual_base64?
self.qual.match(/[K-h]/) ? true : false
end
- # Method to determine if a quality score is valid.
+ # Method to determine if a quality score is valid accepting only 0-40 range.
def qual_valid?(encoding)
raise SeqError, "Missing qual" if self.qual.nil?
- case encoding.downcase
- when "sanger" then return true if self.qual.match(/^[!-~]*$/)
- when "454" then return true if self.qual.match(/^[@-~]*$/)
- when "solexa" then return true if self.qual.match(/^[;-~]*$/)
- when "illumina13" then return true if self.qual.match(/^[@-~]*$/)
- when "illumina15" then return true if self.qual.match(/^[@-~]*$/)
- when "illumina18" then return true if self.qual.match(/^[!-~]*$/)
+ case encoding
+ when :base_33 then return true if self.qual.match(/^[!-I]*$/)
+ when :base_64 then return true if self.qual.match(/^[@-h]*$/)
else raise SeqError, "unknown quality score encoding: #{encoding}"
end
false
end
- # Method to convert quality scores inbetween formats.
- # Sanger base 33, range 0-40
- # 454 base 64, range 0-40
- # Solexa base 64, range -5-40
- # Illumina13 base 64, range 0-40
- # Illumina15 base 64, range 0-40
- # Illumina18 base 33, range 0-41
- def convert_scores!(from, to)
- unless from == to
- na_qual = NArray.to_na(self.qual, "byte")
+ # Method to coerce quality scores to be within the 0-40 range.
+ def qual_coerce!(encoding)
+ raise SeqError, "Missing qual" if self.qual.nil?
- case from.downcase
- when "sanger" then na_qual -= 33
- when "454" then na_qual -= 64
- when "solexa" then na_qual -= 64
- when "illumina13" then na_qual -= 64
- when "illumina15" then na_qual -= 64
- when "illumina18" then na_qual -= 33
- else raise SeqError, "unknown quality score encoding: #{from}"
- end
+ case encoding
+ when :base_33 then self.qual.tr!("[J-~]", "I")
+ when :base_64 then self.qual.tr!("[i-~]", "h")
+ else raise SeqError, "unknown quality score encoding: #{encoding}"
+ end
- case to.downcase
- when "sanger" then na_qual += 33
- when "454" then na_qual += 64
- when "solexa" then na_qual += 64
- when "illumina13" then na_qual += 64
- when "illumina15" then na_qual += 64
- when "illumina18" then na_qual += 33
- else raise SeqError, "unknown quality score encoding: #{to}"
- end
+ self
+ end
+
+ # Method to convert quality scores.
+ def qual_convert!(from, to)
+ raise SeqError, "unknown quality score encoding: #{from}" unless from == :base_33 or from == :base_64
+ raise SeqError, "unknown quality score encoding: #{to}" unless to == :base_33 or to == :base_64
+ if from == :base_33 and to == :base_64
+ na_qual = NArray.to_na(self.qual, "byte")
+ na_qual += 64 - 33
+ self.qual = na_qual.to_s
+ elsif from == :base_64 and to == :base_33
+ self.qual.tr!("[;-?]", "@") # Handle negative Solexa values from -5 to -1 (set these to 0).
+ na_qual = NArray.to_na(self.qual, "byte")
+ na_qual -= 64 - 33
self.qual = na_qual.to_s
end
na_qual = NArray.to_na(self.qual, "byte")
na_qual -= SCORE_BASE
+
na_qual.mean
end
projects / biopieces.git / blobdiff