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'
31 autoload :Dynamic, 'maasha/seq/dynamic'
32 autoload :Homopolymer, 'maasha/seq/homopolymer'
33 autoload :Levenshtein, 'maasha/seq/levenshtein'
38 PROTEIN = %w[f l s y c w p h q r i m t n k v a d e g]
41 # Translation table 11
42 # (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG11)
43 # AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
44 # Starts = ---M---------------M------------MMMM---------------M------------
45 # Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
46 # Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
47 # Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
49 "TTG" => "M", "CTG" => "M", "ATT" => "M", "ATC" => "M",
50 "ATA" => "M", "ATG" => "M", "GTG" => "M"
54 "TTT" => "F", "TCT" => "S", "TAT" => "Y", "TGT" => "C",
55 "TTC" => "F", "TCC" => "S", "TAC" => "Y", "TGC" => "C",
56 "TTA" => "L", "TCA" => "S", "TAA" => "*", "TGA" => "*",
57 "TTG" => "L", "TCG" => "S", "TAG" => "*", "TGG" => "W",
58 "CTT" => "L", "CCT" => "P", "CAT" => "H", "CGT" => "R",
59 "CTC" => "L", "CCC" => "P", "CAC" => "H", "CGC" => "R",
60 "CTA" => "L", "CCA" => "P", "CAA" => "Q", "CGA" => "R",
61 "CTG" => "L", "CCG" => "P", "CAG" => "Q", "CGG" => "R",
62 "ATT" => "I", "ACT" => "T", "AAT" => "N", "AGT" => "S",
63 "ATC" => "I", "ACC" => "T", "AAC" => "N", "AGC" => "S",
64 "ATA" => "I", "ACA" => "T", "AAA" => "K", "AGA" => "R",
65 "ATG" => "M", "ACG" => "T", "AAG" => "K", "AGG" => "R",
66 "GTT" => "V", "GCT" => "A", "GAT" => "D", "GGT" => "G",
67 "GTC" => "V", "GCC" => "A", "GAC" => "D", "GGC" => "G",
68 "GTA" => "V", "GCA" => "A", "GAA" => "E", "GGA" => "G",
69 "GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
72 # Error class for all exceptions to do with Seq.
73 class SeqError < StandardError; end
76 # Quality scores bases
84 attr_accessor :seq_name, :seq, :type, :qual
86 # Class method to instantiate a new Sequence object given
88 def self.new_bp(record)
89 seq_name = record[:SEQ_NAME]
91 type = record[:SEQ_TYPE].to_sym if record[:SEQ_TYPE]
92 qual = record[:SCORES]
94 self.new(seq_name, seq, type, qual)
97 # Class method that generates all possible oligos of a specifed length and type.
98 def self.generate_oligos(length, type)
99 raise SeqError, "Cannot generate negative oligo length: #{length}" if length <= 0
102 when :dna then alph = DNA
103 when :rna then alph = RNA
104 when :protein then alph = PROTEIN
106 raise SeqError, "Unknown sequence type: #{type}"
111 (1 .. length).each do
114 oligos.each do |oligo|
126 # Initialize a sequence object with the following arguments:
127 # - seq_name: Name of the sequence.
128 # - seq: The sequence.
129 # - type: The sequence type - DNA, RNA, or protein
130 # - qual: An Illumina type quality scores string.
131 def initialize(seq_name = nil, seq = nil, type = nil, qual = nil)
138 # Method that guesses and returns the sequence type
139 # by inspecting the first 100 residues.
141 raise SeqError, "Guess failed: sequence is nil" if self.seq.nil?
143 case self.seq[0 ... 100].downcase
144 when /[flpqie]/ then return :protein
145 when /[u]/ then return :rna
150 # Method that guesses and sets the sequence type
151 # by inspecting the first 100 residues.
153 self.type = self.type_guess
157 # Returns the length of a sequence.
159 self.seq.nil? ? 0 : self.seq.length
164 # Return the number indels in a sequence.
166 regex = Regexp.new(/[#{Regexp.escape(INDELS.join(""))}]/)
167 self.seq.scan(regex).size
170 # Method to remove indels from seq and qual if qual.
173 self.seq.delete!(Regexp.escape(INDELS.join('')))
175 na_seq = NArray.to_na(self.seq, "byte")
176 na_qual = NArray.to_na(self.qual, "byte")
177 mask = NArray.byte(self.length)
180 mask += na_seq.eq(c.ord)
185 self.seq = na_seq[mask].to_s
186 self.qual = na_qual[mask].to_s
192 # Method that returns true is a given sequence type is DNA.
197 # Method that returns true is a given sequence type is RNA.
202 # Method that returns true is a given sequence type is protein.
204 self.type == :protein
207 # Method to transcribe DNA to RNA.
209 raise SeqError, "Cannot transcribe 0 length sequence" if self.length == 0
210 raise SeqError, "Cannot transcribe sequence type: #{self.type}" unless self.is_dna?
212 self.seq.tr!('Tt','Uu')
215 # Method to reverse-transcribe RNA to DNA.
217 raise SeqError, "Cannot reverse-transcribe 0 length sequence" if self.length == 0
218 raise SeqError, "Cannot reverse-transcribe sequence type: #{self.type}" unless self.is_rna?
220 self.seq.tr!('Uu','Tt')
223 # Method to translate a DNA sequence to protein.
224 def translate!(trans_tab = 11)
225 raise SeqError, "Sequence type must be 'dna' - not #{self.type}" unless self.type == :dna
226 raise SeqError, "Sequence length must be a multiplum of 3 - was: #{self.length}" unless (self.length % 3) == 0
230 codon_start_hash = TRANS_TAB11_START
231 codon_hash = TRANS_TAB11
233 raise SeqError, "Unknown translation table: #{trans_tab}"
236 codon = self.seq[0 ... 3].upcase
238 aa = codon_start_hash[codon]
240 raise SeqError, "Unknown start codon: #{codon}" if aa.nil?
246 while i < self.length
247 codon = self.seq[i ... i + 3].upcase
249 aa = codon_hash[codon]
251 raise SeqError, "Unknown codon: #{codon}" if aa.nil?
265 alias :to_protein! :translate!
267 def translate(trans_tab = 11)
268 self.dup.translate!(trans_tab)
271 alias :to_protein :translate
273 # Method that given a Seq entry returns a Biopieces record (a hash).
275 raise SeqError, "Missing seq_name" if self.seq_name.nil?
276 raise SeqError, "Missing seq" if self.seq.nil?
279 record[:SEQ_NAME] = self.seq_name
280 record[:SEQ] = self.seq
281 record[:SEQ_LEN] = self.length
282 record[:SCORES] = self.qual if self.qual
286 # Method that given a Seq entry returns a FASTA entry (a string).
287 def to_fasta(wrap = nil)
288 raise SeqError, "Missing seq_name" if self.seq_name.nil? or self.seq_name == ''
289 raise SeqError, "Missing seq" if self.seq.nil? or self.seq.empty?
291 seq_name = self.seq_name.to_s
295 seq.gsub!(/(.{#{wrap}})/) do |match|
302 ">" + seq_name + $/ + seq + $/
305 # Method that given a Seq entry returns a FASTQ entry (a string).
307 raise SeqError, "Missing seq_name" if self.seq_name.nil?
308 raise SeqError, "Missing seq" if self.seq.nil?
309 raise SeqError, "Missing qual" if self.qual.nil?
311 seq_name = self.seq_name.to_s
313 qual = self.qual.to_s
315 "@" + seq_name + $/ + seq + $/ + "+" + $/ + qual + $/
318 # Method that generates a unique key for a
319 # DNA sequence and return this key as a Fixnum.
323 self.seq.upcase.each_char do |char|
327 when 'A' then key |= 0
328 when 'C' then key |= 1
329 when 'G' then key |= 2
330 when 'T' then key |= 3
331 else raise SeqError, "Bad residue: #{char}"
338 # Method to reverse the sequence.
340 Seq.new(self.seq_name, self.seq.reverse, self.type, self.qual ? self.qual.reverse : self.qual)
343 # Method to reverse the sequence.
346 self.qual.reverse! if self.qual
350 # Method that complements sequence including ambiguity codes.
352 raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
355 entry.seq_name = self.seq_name
356 entry.type = self.type
357 entry.qual = self.qual
360 entry.seq = self.seq.tr('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
362 entry.seq = self.seq.tr('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn')
364 raise SeqError, "Cannot complement sequence type: #{self.type}"
370 # Method that complements sequence including ambiguity codes.
372 raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
375 self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
377 self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn')
379 raise SeqError, "Cannot complement sequence type: #{self.type}"
385 # Method to determine the Hamming Distance between
386 # two Sequence objects (case insensitive).
387 def hamming_distance(entry)
388 self.seq.upcase.hamming_distance(entry.seq.upcase)
391 # Method to determine the Edit Distance between
392 # two Sequence objects (case insensitive).
393 def edit_distance(entry)
394 Levenshtein.distance(self.seq, entry.seq)
397 # Method that generates a random sequence of a given length and type.
398 def generate(length, type)
399 raise SeqError, "Cannot generate sequence length < 1: #{length}" if length <= 0
402 when :dna then alph = DNA
403 when :rna then alph = RNA
404 when :protein then alph = PROTEIN
406 raise SeqError, "Unknown sequence type: #{type}"
409 seq_new = Array.new(length) { alph[rand(alph.size)] }.join("")
415 # Method to return a new Seq object with shuffled sequence.
417 Seq.new(self.seq_name, self.seq.split('').shuffle!.join, self.type, self.qual)
420 # Method to shuffle a sequence randomly inline.
422 self.seq = self.seq.split('').shuffle!.join
426 # Method to add two Seq objects.
428 new_entry = Seq.new()
429 new_entry.seq = self.seq + entry.seq
430 new_entry.type = self.type if self.type == entry.type
431 new_entry.qual = self.qual + entry.qual if self.qual and entry.qual
435 # Method to concatenate sequence entries.
437 raise SeqError, "sequences of different types" unless self.type == entry.type
438 raise SeqError, "qual is missing in one entry" unless self.qual.class == entry.qual.class
440 self.seq << entry.seq
441 self.qual << entry.qual unless entry.qual.nil?
446 # Index method for Seq objects.
449 entry.seq_name = self.seq_name
450 entry.seq = self.seq[*args]
451 entry.type = self.type
452 entry.qual = self.qual[*args] unless self.qual.nil?
457 # Index assignment method for Seq objects.
458 def []=(*args, entry)
459 self.seq[*args] = entry.seq[*args]
460 self.qual[*args] = entry.qual[*args] unless self.qual.nil?
465 # Method that returns a subsequence of from a given start position
466 # and of a given length.
467 def subseq(start, length = self.length - start)
468 raise SeqError, "subsequence start: #{start} < 0" if start < 0
469 raise SeqError, "subsequence length: #{length} < 0" if length < 0
470 raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
474 qual = "" unless self.qual.nil?
476 stop = start + length - 1
478 seq = self.seq[start .. stop]
479 qual = self.qual[start .. stop] unless self.qual.nil?
482 seq_name = self.seq_name.nil? ? nil : self.seq_name.dup
484 Seq.new(seq_name, seq, self.type, qual)
487 # Method that replaces a sequence with a subsequence from a given start position
488 # and of a given length.
489 def subseq!(start, length = self.length - start)
490 s = subseq(start, length)
492 self.seq_name = s.seq_name
500 # Method that returns a subsequence of a given length
501 # beginning at a random position.
502 def subseq_rand(length)
503 if self.length - length + 1 == 0
506 start = rand(self.length - length + 1)
509 self.subseq(start, length)
512 # Method that returns the residue compositions of a sequence in
513 # a hash where the key is the residue and the value is the residue
518 self.seq.upcase.each_char do |char|
525 # Method that returns the percentage of hard masked residues
526 # or N's in a sequence.
528 ((self.seq.upcase.scan("N").size.to_f / (self.len - self.indels).to_f) * 100).round(2)
531 # Method that returns the percentage of soft masked residues
532 # or lower cased residues in a sequence.
534 ((self.seq.scan(/[a-z]/).size.to_f / (self.len - self.indels).to_f) * 100).round(2)
537 # Hard masks sequence residues where the corresponding quality score
538 # is below a given cutoff.
539 def mask_seq_hard!(cutoff)
540 raise SeqError, "seq is nil" if self.seq.nil?
541 raise SeqError, "qual is nil" if self.qual.nil?
542 raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
544 na_seq = NArray.to_na(self.seq, "byte")
545 na_qual = NArray.to_na(self.qual, "byte")
546 mask = (na_qual - SCORE_BASE) < cutoff
547 mask *= na_seq.ne("-".ord)
549 na_seq[mask] = 'N'.ord
551 self.seq = na_seq.to_s
556 # Soft masks sequence residues where the corresponding quality score
557 # is below a given cutoff.
558 def mask_seq_soft!(cutoff)
559 raise SeqError, "seq is nil" if self.seq.nil?
560 raise SeqError, "qual is nil" if self.qual.nil?
561 raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
563 na_seq = NArray.to_na(self.seq, "byte")
564 na_qual = NArray.to_na(self.qual, "byte")
565 mask = (na_qual - SCORE_BASE) < cutoff
566 mask *= na_seq.ne("-".ord)
568 na_seq[mask] ^= ' '.ord
570 self.seq = na_seq.to_s
575 # Method that determines if a quality score string can be
576 # absolutely identified as base 33.
578 self.qual.match(/[!-:]/) ? true : false
581 # Method that determines if a quality score string may be base 64.
583 self.qual.match(/[K-h]/) ? true : false
586 # Method to determine if a quality score is valid accepting only 0-40 range.
587 def qual_valid?(encoding)
588 raise SeqError, "Missing qual" if self.qual.nil?
591 when :base_33 then return true if self.qual.match(/^[!-I]*$/)
592 when :base_64 then return true if self.qual.match(/^[@-h]*$/)
593 else raise SeqError, "unknown quality score encoding: #{encoding}"
599 # Method to coerce quality scores to be within the 0-40 range.
600 def qual_coerce!(encoding)
601 raise SeqError, "Missing qual" if self.qual.nil?
604 when :base_33 then self.qual.tr!("[J-~]", "I")
605 when :base_64 then self.qual.tr!("[i-~]", "h")
606 else raise SeqError, "unknown quality score encoding: #{encoding}"
612 # Method to convert quality scores.
613 def qual_convert!(from, to)
614 raise SeqError, "unknown quality score encoding: #{from}" unless from == :base_33 or from == :base_64
615 raise SeqError, "unknown quality score encoding: #{to}" unless to == :base_33 or to == :base_64
617 if from == :base_33 and to == :base_64
618 na_qual = NArray.to_na(self.qual, "byte")
620 self.qual = na_qual.to_s
621 elsif from == :base_64 and to == :base_33
622 self.qual.tr!("[;-?]", "@") # Handle negative Solexa values from -5 to -1 (set these to 0).
623 na_qual = NArray.to_na(self.qual, "byte")
625 self.qual = na_qual.to_s
631 # Method to calculate and return the mean quality score.
633 raise SeqError, "Missing qual in entry" if self.qual.nil?
635 na_qual = NArray.to_na(self.qual, "byte")
636 na_qual -= SCORE_BASE
641 # Method to find open reading frames (ORFs).
642 def each_orf(size_min, size_max, start_codons, stop_codons, pick_longest = false)
646 regex_start = Regexp.new(start_codons.join('|'), true)
647 regex_stop = Regexp.new(stop_codons.join('|'), true)
649 while pos_beg and pos_beg < self.length - size_min
650 if pos_beg = self.seq.index(regex_start, pos_beg)
651 if pos_end = self.seq.index(regex_stop, pos_beg)
652 length = (pos_end - pos_beg) + 3
655 if size_min <= length and length <= size_max
656 subseq = self.subseq(pos_beg, length)
658 orfs << [subseq, pos_beg, pos_end + 3]
670 orfs.each { |orf| orf_hash[orf.last] = orf unless orf_hash[orf.last] }
672 orfs = orf_hash.values
676 orfs.each { |orf| yield orf }