# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
require 'maasha/bits'
-require 'maasha/seq/backtrack'
require 'maasha/seq/digest'
-#require 'maasha/seq/patscan'
-require 'maasha/seq/patternmatcher'
require 'maasha/seq/trim'
require 'narray'
+autoload :BackTrack, 'maasha/seq/backtrack.rb'
+autoload :Dynamic, 'maasha/seq/dynamic.rb'
+
# Residue alphabets
DNA = %w[a t c g]
RNA = %w[a u 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[. - _ ~]
-# Quality scores bases
-SCORE_BASE = 64
-SCORE_MIN = 0
-SCORE_MAX = 40
+# 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"
+}
+
# Error class for all exceptions to do with Seq.
class SeqError < StandardError; end
class Seq
- #include Patscan
- include PatternMatcher
- include BackTrack
+ # Quality scores bases
+ SCORE_BASE = 64
+ SCORE_MIN = 0
+ SCORE_MAX = 40
+
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?
seq_new
end
- # Method to shuffle a sequence readomly inline.
+ # Method to return a new Seq object with shuffled sequence.
+ def shuffle
+ Seq.new(self.seq_name, self.seq.split('').shuffle!.join, self.type, self.qual)
+ end
+
+ # Method to shuffle a sequence randomly inline.
def shuffle!
self.seq = self.seq.split('').shuffle!.join
self
qual = self.qual[start .. stop] unless self.qual.nil?
end
- Seq.new(self.seq_name.dup, 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(/[!-:]/) ? true : false
+ end
+
+ # Method that determines if a quality score string can be
+ # absolutely identified as base 64.
+ def qual_base64?
+ self.qual.match(/[K-h]/) ? true : false
+ end
+
+ # Method to determine if a quality score is valid.
+ 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(/^[@-~]*$/)
+ when "illumina18" then return true if self.qual.match(/^[!-~]*$/)
+ 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 3-40
+ # Illumina15 base 64, range 0-40
# Illumina18 base 33, range 0-41
def convert_scores!(from, to)
unless from == to
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
when "illumina18" then na_qual += 33
- else raise SeqError, "unknown quality score encoding: #{from}"
+ else raise SeqError, "unknown quality score encoding: #{to}"
end
self.qual = na_qual.to_s
if pos_end = self.seq.index(regex_stop, pos_beg)
length = (pos_end - pos_beg) + 3
- if size_min <= length and length <= size_max
- subseq = self.subseq(pos_beg, length)
+ 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]
+ orfs << [subseq, pos_beg, pos_end + 3]
+ end
end
end
if pick_longest
orf_hash = {}
- orfs.each { |orf| orf_hash[orf.last] = orf }
+ orfs.each { |orf| orf_hash[orf.last] = orf unless orf_hash[orf.last] }
orfs = orf_hash.values
end
projects / biopieces.git / blobdiff