1 # Copyright (C) 2007-2012 Martin A. Hansen.
3 # This program is free software; you can redistribute it and/or
4 # modify it under the terms of the GNU General Public License
5 # as published by the Free Software Foundation; either version 2
6 # of the License, or (at your option) any later version.
8 # This program is distributed in the hope that it will be useful,
9 # but WITHOUT ANY WARRANTY; without even the implied warranty of
10 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
11 # GNU General Public License for more details.
13 # You should have received a copy of the GNU General Public License
14 # along with this program; if not, write to the Free Software
15 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
17 # http://www.gnu.org/copyleft/gpl.html
19 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
21 # This software is part of the Biopieces framework (www.biopieces.org).
23 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
26 require 'maasha/seq/digest'
27 require 'maasha/seq/trim'
30 autoload :BackTrack, 'maasha/seq/backtrack.rb'
31 autoload :Dynamic, 'maasha/seq/dynamic.rb'
36 PROTEIN = %w[f l s y c w p h q r i m t n k v a d e g]
39 # Translation table 11
40 # (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG11)
41 # AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
42 # Starts = ---M---------------M------------MMMM---------------M------------
43 # Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
44 # Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
45 # Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
47 "TTG" => "M", "CTG" => "M", "ATT" => "M", "ATC" => "M",
48 "ATA" => "M", "ATG" => "M", "GTG" => "M"
52 "TTT" => "F", "TCT" => "S", "TAT" => "Y", "TGT" => "C",
53 "TTC" => "F", "TCC" => "S", "TAC" => "Y", "TGC" => "C",
54 "TTA" => "L", "TCA" => "S", "TAA" => "*", "TGA" => "*",
55 "TTG" => "L", "TCG" => "S", "TAG" => "*", "TGG" => "W",
56 "CTT" => "L", "CCT" => "P", "CAT" => "H", "CGT" => "R",
57 "CTC" => "L", "CCC" => "P", "CAC" => "H", "CGC" => "R",
58 "CTA" => "L", "CCA" => "P", "CAA" => "Q", "CGA" => "R",
59 "CTG" => "L", "CCG" => "P", "CAG" => "Q", "CGG" => "R",
60 "ATT" => "I", "ACT" => "T", "AAT" => "N", "AGT" => "S",
61 "ATC" => "I", "ACC" => "T", "AAC" => "N", "AGC" => "S",
62 "ATA" => "I", "ACA" => "T", "AAA" => "K", "AGA" => "R",
63 "ATG" => "M", "ACG" => "T", "AAG" => "K", "AGG" => "R",
64 "GTT" => "V", "GCT" => "A", "GAT" => "D", "GGT" => "G",
65 "GTC" => "V", "GCC" => "A", "GAC" => "D", "GGC" => "G",
66 "GTA" => "V", "GCA" => "A", "GAA" => "E", "GGA" => "G",
67 "GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
70 # Quality scores bases
75 # Error class for all exceptions to do with Seq.
76 class SeqError < StandardError; end
82 attr_accessor :seq_name, :seq, :type, :qual
84 # Class method to instantiate a new Sequence object given
86 def self.new_bp(record)
87 seq_name = record[:SEQ_NAME]
89 type = record[:SEQ_TYPE]
90 qual = record[:SCORES]
92 self.new(seq_name, seq, type, qual)
95 # Class method that generates all possible oligos of a specifed length and type.
96 def self.generate_oligos(length, type)
97 raise SeqError, "Cannot generate negative oligo length: #{length}" if length <= 0
100 when /dna/ then alph = DNA
101 when /rna/ then alph = RNA
102 when /protein/ then alph = PROTEIN
104 raise SeqError, "Unknown sequence type: #{type}"
109 (1 .. length).each do
112 oligos.each do |oligo|
124 # Initialize a sequence object with the following arguments:
125 # - seq_name: Name of the sequence.
126 # - seq: The sequence.
127 # - type: The sequence type - DNA, RNA, or protein
128 # - qual: An Illumina type quality scores string.
129 def initialize(seq_name = nil, seq = nil, type = nil, qual = nil)
136 # Method that guesses and returns the sequence type
137 # by inspecting the first 100 residues.
139 raise SeqError, "Guess failed: sequence is nil" if self.seq.nil?
141 case self.seq[0 ... 100].downcase
142 when /[flpqie]/ then return "protein"
143 when /[u]/ then return "rna"
148 # Method that guesses and sets the sequence type
149 # by inspecting the first 100 residues.
151 self.type = self.type_guess
154 # Returns the length of a sequence.
156 self.seq.nil? ? 0 : self.seq.length
161 # Return the number indels in a sequence.
163 regex = Regexp.new(/[#{Regexp.escape(INDELS.join(""))}]/)
164 self.seq.scan(regex).size
167 # Method to remove indels from seq and qual if qual.
170 self.seq.delete!(Regexp.escape(INDELS.join('')))
172 na_seq = NArray.to_na(self.seq, "byte")
173 na_qual = NArray.to_na(self.qual, "byte")
174 mask = NArray.byte(self.length)
177 mask += na_seq.eq(c.ord)
182 self.seq = na_seq[mask].to_s
183 self.qual = na_qual[mask].to_s
189 # Method that returns true is a given sequence type is DNA.
194 # Method that returns true is a given sequence type is RNA.
199 # Method that returns true is a given sequence type is protein.
201 self.type == 'protein'
204 # Method to transcribe DNA to RNA.
206 raise SeqError, "Cannot transcribe 0 length sequence" if self.length == 0
207 raise SeqError, "Cannot transcribe sequence type: #{self.type}" unless self.is_dna?
209 self.seq.tr!('Tt','Uu')
212 # Method to reverse-transcribe RNA to DNA.
214 raise SeqError, "Cannot reverse-transcribe 0 length sequence" if self.length == 0
215 raise SeqError, "Cannot reverse-transcribe sequence type: #{self.type}" unless self.is_rna?
218 self.seq.tr!('Uu','Tt')
221 # Method to translate a DNA sequence to protein.
222 def translate!(trans_tab = 11)
223 raise SeqError, "Sequence type must be 'dna' - not #{self.type}" unless self.type == 'dna'
224 raise SeqError, "Sequence length must be a multiplum of 3 - was: #{self.length}" unless (self.length % 3) == 0
228 codon_start_hash = TRANS_TAB11_START
229 codon_hash = TRANS_TAB11
231 raise SeqError, "Unknown translation table: #{trans_tab}"
234 codon = self.seq[0 ... 3].upcase
236 aa = codon_start_hash[codon]
238 raise SeqError, "Unknown start codon: #{codon}" if aa.nil?
244 while i < self.length
245 codon = self.seq[i ... i + 3].upcase
247 aa = codon_hash[codon]
249 raise SeqError, "Unknown codon: #{codon}" if aa.nil?
258 self.type = "protein"
263 alias :to_protein! :translate!
265 def translate(trans_tab = 11)
266 self.dup.translate!(trans_tab)
269 alias :to_protein :translate
271 # Method that given a Seq entry returns a Biopieces record (a hash).
273 raise SeqError, "Missing seq_name" if self.seq_name.nil?
274 raise SeqError, "Missing seq" if self.seq.nil?
277 record[:SEQ_NAME] = self.seq_name
278 record[:SEQ] = self.seq
279 record[:SEQ_LEN] = self.length
280 record[:SCORES] = self.qual if self.qual
284 # Method that given a Seq entry returns a FASTA entry (a string).
285 def to_fasta(wrap = nil)
286 raise SeqError, "Missing seq_name" if self.seq_name.nil? or self.seq_name == ''
287 raise SeqError, "Missing seq" if self.seq.nil? or self.seq.empty?
289 seq_name = self.seq_name.to_s
293 seq.gsub!(/(.{#{wrap}})/) do |match|
300 ">" + seq_name + $/ + seq + $/
303 # Method that given a Seq entry returns a FASTQ entry (a string).
305 raise SeqError, "Missing seq_name" if self.seq_name.nil?
306 raise SeqError, "Missing seq" if self.seq.nil?
307 raise SeqError, "Missing qual" if self.qual.nil?
309 seq_name = self.seq_name.to_s
311 qual = self.qual.to_s
313 "@" + seq_name + $/ + seq + $/ + "+" + $/ + qual + $/
316 # Method that generates a unique key for a
317 # DNA sequence and return this key as a Fixnum.
321 self.seq.upcase.each_char do |char|
325 when 'A' then key |= 0
326 when 'C' then key |= 1
327 when 'G' then key |= 2
328 when 'T' then key |= 3
329 else raise SeqError, "Bad residue: #{char}"
336 # Method to reverse complement sequence.
337 def reverse_complement
343 alias :revcomp :reverse_complement
345 # Method to reverse the sequence.
348 self.qual.reverse! if self.qual
352 # Method that complements sequence including ambiguity codes.
354 raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
357 self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
359 self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn')
361 raise SeqError, "Cannot complement sequence type: #{self.type}"
365 # Method to determine the Hamming Distance between
366 # two Sequence objects (case insensitive).
367 def hamming_distance(seq)
368 self.seq.upcase.hamming_distance(seq.seq.upcase)
371 # Method that generates a random sequence of a given length and type.
372 def generate(length, type)
373 raise SeqError, "Cannot generate sequence length < 1: #{length}" if length <= 0
383 raise SeqError, "Unknown sequence type: #{type}"
386 seq_new = Array.new(length) { alph[rand(alph.size)] }.join("")
388 self.type = type.downcase
392 # Method to shuffle a sequence readomly inline.
394 self.seq = self.seq.split('').shuffle!.join
398 # Method that returns a subsequence of from a given start position
399 # and of a given length.
400 def subseq(start, length = self.length - start)
401 raise SeqError, "subsequence start: #{start} < 0" if start < 0
402 raise SeqError, "subsequence length: #{length} < 0" if length < 0
403 raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
407 qual = "" unless self.qual.nil?
409 stop = start + length - 1
411 seq = self.seq[start .. stop]
412 qual = self.qual[start .. stop] unless self.qual.nil?
415 Seq.new(self.seq_name, seq, self.type, qual) # TODO changed self.seq_name.dup to self.seq_name -> consequence?
418 # Method that replaces a sequence with a subsequence from a given start position
419 # and of a given length.
420 def subseq!(start, length = self.length - start)
421 s = subseq(start, length)
423 self.seq_name = s.seq_name
431 # Method that returns a subsequence of a given length
432 # beginning at a random position.
433 def subseq_rand(length)
434 if self.length - length + 1 == 0
437 start = rand(self.length - length + 1)
440 self.subseq(start, length)
443 # Method that returns the residue compositions of a sequence in
444 # a hash where the key is the residue and the value is the residue
449 self.seq.upcase.each_char do |char|
456 # Method that returns the length of the longest homopolymeric stretch
457 # found in a sequence.
458 def homopol_max(min = 1)
459 return 0 if self.seq.nil? or self.seq.empty?
463 self.seq.upcase.scan(/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/) do |match|
465 min = match.size > min ? match.size : min
468 return 0 unless found
473 # Method that returns the percentage of hard masked residues
474 # or N's in a sequence.
476 ((self.seq.upcase.scan("N").size.to_f / (self.len - self.indels).to_f) * 100).round(2)
479 # Method that returns the percentage of soft masked residues
480 # or lower cased residues in a sequence.
482 ((self.seq.scan(/[a-z]/).size.to_f / (self.len - self.indels).to_f) * 100).round(2)
485 # Hard masks sequence residues where the corresponding quality score
486 # is below a given cutoff.
487 def mask_seq_hard_old(cutoff)
488 seq = self.seq.upcase
492 scores.each_char do |score|
493 seq[i] = 'N' if score.ord - SCORE_BASE < cutoff
500 # Hard masks sequence residues where the corresponding quality score
501 # is below a given cutoff.
502 def mask_seq_hard!(cutoff)
503 raise SeqError, "seq is nil" if self.seq.nil?
504 raise SeqError, "qual is nil" if self.qual.nil?
505 raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
507 na_seq = NArray.to_na(self.seq, "byte")
508 na_qual = NArray.to_na(self.qual, "byte")
509 mask = (na_qual - SCORE_BASE) < cutoff
510 mask *= na_seq.ne("-".ord)
512 na_seq[mask] = 'N'.ord
514 self.seq = na_seq.to_s
519 # Soft masks sequence residues where the corresponding quality score
520 # is below a given cutoff.
521 def mask_seq_soft!(cutoff)
522 raise SeqError, "seq is nil" if self.seq.nil?
523 raise SeqError, "qual is nil" if self.qual.nil?
524 raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
526 na_seq = NArray.to_na(self.seq, "byte")
527 na_qual = NArray.to_na(self.qual, "byte")
528 mask = (na_qual - SCORE_BASE) < cutoff
529 mask *= na_seq.ne("-".ord)
531 na_seq[mask] ^= ' '.ord
533 self.seq = na_seq.to_s
538 # Method that determines if a quality score string can be
539 # absolutely identified as base 33.
541 self.qual.match(/[!-:]/) ? true : false
544 # Method that determines if a quality score string can be
545 # absolutely identified as base 64.
547 self.qual.match(/[K-h]/) ? true : false
550 # Method to determine if a quality score is valid.
551 def qual_valid?(encoding)
552 raise SeqError, "Missing qual" if self.qual.nil?
554 case encoding.downcase
555 when "sanger" then return true if self.qual.match(/^[!-I]*$/)
556 when "454" then return true if self.qual.match(/^[@-h]*$/)
557 when "solexa" then return true if self.qual.match(/^[;-h]*$/)
558 when "illumina13" then return true if self.qual.match(/^[@-h]*$/)
559 when "illumina15" then return true if self.qual.match(/^[@-h]*$/)
560 when "illumina18" then return true if self.qual.match(/^[!-J]*$/)
561 else raise SeqError, "unknown quality score encoding: #{encoding}"
567 # Method to convert quality scores inbetween formats.
568 # Sanger base 33, range 0-40
569 # 454 base 64, range 0-40
570 # Solexa base 64, range -5-40
571 # Illumina13 base 64, range 0-40
572 # Illumina15 base 64, range 0-40
573 # Illumina18 base 33, range 0-41
574 def convert_scores!(from, to)
576 na_qual = NArray.to_na(self.qual, "byte")
579 when "sanger" then na_qual -= 33
580 when "454" then na_qual -= 64
581 when "solexa" then na_qual -= 64
582 when "illumina13" then na_qual -= 64
583 when "illumina15" then na_qual -= 64
584 when "illumina18" then na_qual -= 33
585 else raise SeqError, "unknown quality score encoding: #{from}"
589 when "sanger" then na_qual += 33
590 when "454" then na_qual += 64
591 when "solexa" then na_qual += 64
592 when "illumina13" then na_qual += 64
593 when "illumina15" then na_qual += 64
594 when "illumina18" then na_qual += 33
595 else raise SeqError, "unknown quality score encoding: #{to}"
598 self.qual = na_qual.to_s
604 # Method to calculate and return the mean quality score.
606 raise SeqError, "Missing qual in entry" if self.qual.nil?
608 na_qual = NArray.to_na(self.qual, "byte")
609 na_qual -= SCORE_BASE
613 # Method to find open reading frames (ORFs).
614 def each_orf(size_min, size_max, start_codons, stop_codons, pick_longest = false)
618 regex_start = Regexp.new(start_codons.join('|'), true)
619 regex_stop = Regexp.new(stop_codons.join('|'), true)
621 while pos_beg and pos_beg < self.length - size_min
622 if pos_beg = self.seq.index(regex_start, pos_beg)
623 if pos_end = self.seq.index(regex_stop, pos_beg)
624 length = (pos_end - pos_beg) + 3
627 if size_min <= length and length <= size_max
628 subseq = self.subseq(pos_beg, length)
630 orfs << [subseq, pos_beg, pos_end + 3]
642 orfs.each { |orf| orf_hash[orf.last] = orf unless orf_hash[orf.last] }
644 orfs = orf_hash.values
648 orfs.each { |orf| yield orf }