# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-require 'maasha/patternmatcher'
require 'maasha/bits'
-require 'maasha/backtrack'
-require 'maasha/digest'
+require 'maasha/seq/digest'
require 'maasha/seq/trim'
require 'narray'
-#require 'maasha/patscan'
+
+autoload :BackTrack, 'maasha/seq/backtrack.rb'
+autoload :Dynamic, 'maasha/seq/dynamic.rb'
# Residue alphabets
DNA = %w[a t c g]
PROTEIN = %w[f l s y c w p h q r i m t n k v a d e g]
INDELS = %w[. - _ ~]
+# Translation table 11
+# (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG11)
+# AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+# Starts = ---M---------------M------------MMMM---------------M------------
+# Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+# Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+# Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+TRANS_TAB11_START = {
+ "TTG" => "M", "CTG" => "M", "ATT" => "M", "ATC" => "M",
+ "ATA" => "M", "ATG" => "M", "GTG" => "M"
+}
+
+TRANS_TAB11 = {
+ "TTT" => "F", "TCT" => "S", "TAT" => "Y", "TGT" => "C",
+ "TTC" => "F", "TCC" => "S", "TAC" => "Y", "TGC" => "C",
+ "TTA" => "L", "TCA" => "S", "TAA" => "*", "TGA" => "*",
+ "TTG" => "L", "TCG" => "S", "TAG" => "*", "TGG" => "W",
+ "CTT" => "L", "CCT" => "P", "CAT" => "H", "CGT" => "R",
+ "CTC" => "L", "CCC" => "P", "CAC" => "H", "CGC" => "R",
+ "CTA" => "L", "CCA" => "P", "CAA" => "Q", "CGA" => "R",
+ "CTG" => "L", "CCG" => "P", "CAG" => "Q", "CGG" => "R",
+ "ATT" => "I", "ACT" => "T", "AAT" => "N", "AGT" => "S",
+ "ATC" => "I", "ACC" => "T", "AAC" => "N", "AGC" => "S",
+ "ATA" => "I", "ACA" => "T", "AAA" => "K", "AGA" => "R",
+ "ATG" => "M", "ACG" => "T", "AAG" => "K", "AGG" => "R",
+ "GTT" => "V", "GCT" => "A", "GAT" => "D", "GGT" => "G",
+ "GTC" => "V", "GCC" => "A", "GAC" => "D", "GGC" => "G",
+ "GTA" => "V", "GCA" => "A", "GAA" => "E", "GGA" => "G",
+ "GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
+}
+
# Quality scores bases
SCORE_BASE = 64
SCORE_MIN = 0
class SeqError < StandardError; end
class Seq
- #include Patscan
- include PatternMatcher
- include BackTrack
include Digest
include Trim
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 length must be a multiplum of 3 - was: #{self.length}" unless (self.length % 3) == 0
+
+ case trans_tab
+ when 11
+ codon_start_hash = TRANS_TAB11_START
+ codon_hash = TRANS_TAB11
+ else
+ raise SeqError, "Unknown translation table: #{trans_tab}"
+ end
+
+ codon = self.seq[0 ... 3].upcase
+
+ aa = codon_start_hash[codon]
+
+ raise SeqError, "Unknown start codon: #{codon}" if aa.nil?
+
+ protein = aa
+
+ i = 3
+
+ while i < self.length
+ codon = self.seq[i ... i + 3].upcase
+
+ aa = codon_hash[codon]
+
+ raise SeqError, "Unknown codon: #{codon}" if aa.nil?
+
+ protein << aa
+
+ i += 3
+ end
+
+ self.seq = protein
+ self.qual = nil
+ self.type = "protein"
+
+ self
+ end
+
+ alias :to_protein! :translate!
+
+ def translate(trans_tab = 11)
+ self.dup.translate!(trans_tab)
+ end
+
+ alias :to_protein :translate
+
# Method that given a Seq entry returns a Biopieces record (a hash).
def to_bp
raise SeqError, "Missing seq_name" if self.seq_name.nil?
raise SeqError, "subsequence length: #{length} < 0" if length < 0
raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
-
if length == 0
seq = ""
qual = "" unless self.qual.nil?
qual = self.qual[start .. stop] unless self.qual.nil?
end
-
- Seq.new(self.seq_name, seq, self.type, qual)
+ Seq.new(self.seq_name, seq, self.type, qual) # TODO changed self.seq_name.dup to self.seq_name -> consequence?
end
# Method that replaces a sequence with a subsequence from a given start position
# and of a given length.
def subseq!(start, length = self.length - start)
- raise SeqError, "subsequence start: #{start} < 0" if start < 0
- raise SeqError, "subsequence length: #{length} < 0" if length < 0
- raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
+ s = subseq(start, length)
- if length == 0
- self.seq = ""
- self.qual = "" unless self.qual.nil?
- else
- stop = start + length - 1
-
- self.seq = self.seq[start .. stop]
- self.qual = self.qual[start .. stop] unless self.qual.nil?
- end
+ self.seq_name = s.seq_name
+ self.seq = s.seq
+ self.type = s.type
+ self.qual = s.qual
self
end
self
end
+ # Method that determines if a quality score string can be
+ # absolutely identified as base 33.
+ def qual_base33?
+ self.qual.match(/[!-:]/)
+ end
+
+ # Method that determines if a quality score string can be
+ # absolutely identified as base 64.
+ def qual_base64?
+ self.qual.match(/[K-h]/)
+ 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 3-40
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
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
self
end
+
+ # Method to calculate and return the mean quality score.
+ def scores_mean
+ raise SeqError, "Missing qual in entry" if self.qual.nil?
+
+ na_qual = NArray.to_na(self.qual, "byte")
+ na_qual -= SCORE_BASE
+ na_qual.mean
+ end
+
+ # Method to find open reading frames (ORFs).
+ def each_orf(size_min, size_max, start_codons, stop_codons, pick_longest = false)
+ orfs = []
+ pos_beg = 0
+
+ regex_start = Regexp.new(start_codons.join('|'), true)
+ regex_stop = Regexp.new(stop_codons.join('|'), true)
+
+ while pos_beg and pos_beg < self.length - size_min
+ if pos_beg = self.seq.index(regex_start, pos_beg)
+ if pos_end = self.seq.index(regex_stop, pos_beg)
+ length = (pos_end - pos_beg) + 3
+
+ if (length % 3) == 0
+ if size_min <= length and length <= size_max
+ subseq = self.subseq(pos_beg, length)
+
+ orfs << [subseq, pos_beg, pos_end + 3]
+ end
+ end
+ end
+
+ pos_beg += 1
+ end
+ end
+
+ if pick_longest
+ orf_hash = {}
+
+ orfs.each { |orf| orf_hash[orf.last] = orf unless orf_hash[orf.last] }
+
+ orfs = orf_hash.values
+ end
+
+ if block_given?
+ orfs.each { |orf| yield orf }
+ else
+ return orfs
+ end
+ end
end
__END__