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/backtrack'
27 require 'maasha/seq/digest'
28 #require 'maasha/seq/patscan'
29 require 'maasha/seq/patternmatcher'
30 require 'maasha/seq/trim'
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
80 include PatternMatcher
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]
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
156 # Returns the length of a sequence.
158 self.seq.nil? ? 0 : self.seq.length
163 # Return the number indels in a sequence.
165 regex = Regexp.new(/[#{Regexp.escape(INDELS.join(""))}]/)
166 self.seq.scan(regex).size
169 # Method to remove indels from seq and qual if qual.
172 self.seq.delete!(Regexp.escape(INDELS.join('')))
174 na_seq = NArray.to_na(self.seq, "byte")
175 na_qual = NArray.to_na(self.qual, "byte")
176 mask = NArray.byte(self.length)
179 mask += na_seq.eq(c.ord)
184 self.seq = na_seq[mask].to_s
185 self.qual = na_qual[mask].to_s
191 # Method that returns true is a given sequence type is DNA.
196 # Method that returns true is a given sequence type is RNA.
201 # Method that returns true is a given sequence type is protein.
203 self.type == 'protein'
206 # Method to transcribe DNA to RNA.
208 raise SeqError, "Cannot transcribe 0 length sequence" if self.length == 0
209 raise SeqError, "Cannot transcribe sequence type: #{self.type}" unless self.is_dna?
211 self.seq.tr!('Tt','Uu')
214 # Method to reverse-transcribe RNA to DNA.
216 raise SeqError, "Cannot reverse-transcribe 0 length sequence" if self.length == 0
217 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?
260 self.type = "protein"
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 complement sequence.
339 def reverse_complement
345 alias :revcomp :reverse_complement
347 # Method to reverse the sequence.
350 self.qual.reverse! if self.qual
354 # Method that complements sequence including ambiguity codes.
356 raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
359 self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
361 self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn')
363 raise SeqError, "Cannot complement sequence type: #{self.type}"
367 # Method to determine the Hamming Distance between
368 # two Sequence objects (case insensitive).
369 def hamming_distance(seq)
370 self.seq.upcase.hamming_distance(seq.seq.upcase)
373 # Method that generates a random sequence of a given length and type.
374 def generate(length, type)
375 raise SeqError, "Cannot generate sequence length < 1: #{length}" if length <= 0
385 raise SeqError, "Unknown sequence type: #{type}"
388 seq_new = Array.new(length) { alph[rand(alph.size)] }.join("")
390 self.type = type.downcase
394 # Method to shuffle a sequence readomly inline.
396 self.seq = self.seq.split('').shuffle!.join
400 # Method that returns a subsequence of from a given start position
401 # and of a given length.
402 def subseq(start, length = self.length - start)
403 raise SeqError, "subsequence start: #{start} < 0" if start < 0
404 raise SeqError, "subsequence length: #{length} < 0" if length < 0
405 raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
409 qual = "" unless self.qual.nil?
411 stop = start + length - 1
413 seq = self.seq[start .. stop]
414 qual = self.qual[start .. stop] unless self.qual.nil?
417 Seq.new(self.seq_name, seq, self.type, qual) # TODO changed self.seq_name.dup to self.seq_name -> consequence?
420 # Method that replaces a sequence with a subsequence from a given start position
421 # and of a given length.
422 def subseq!(start, length = self.length - start)
423 s = subseq(start, length)
425 self.seq_name = s.seq_name
433 # Method that returns a subsequence of a given length
434 # beginning at a random position.
435 def subseq_rand(length)
436 if self.length - length + 1 == 0
439 start = rand(self.length - length + 1)
442 self.subseq(start, length)
445 # Method that returns the residue compositions of a sequence in
446 # a hash where the key is the residue and the value is the residue
451 self.seq.upcase.each_char do |char|
458 # Method that returns the length of the longest homopolymeric stretch
459 # found in a sequence.
460 def homopol_max(min = 1)
461 return 0 if self.seq.nil? or self.seq.empty?
465 self.seq.upcase.scan(/A{#{min},}|T{#{min},}|G{#{min},}|C{#{min},}|N{#{min},}/) do |match|
467 min = match.size > min ? match.size : min
470 return 0 unless found
475 # Method that returns the percentage of hard masked residues
476 # or N's in a sequence.
478 ((self.seq.upcase.scan("N").size.to_f / (self.len - self.indels).to_f) * 100).round(2)
481 # Method that returns the percentage of soft masked residues
482 # or lower cased residues in a sequence.
484 ((self.seq.scan(/[a-z]/).size.to_f / (self.len - self.indels).to_f) * 100).round(2)
487 # Hard masks sequence residues where the corresponding quality score
488 # is below a given cutoff.
489 def mask_seq_hard_old(cutoff)
490 seq = self.seq.upcase
494 scores.each_char do |score|
495 seq[i] = 'N' if score.ord - SCORE_BASE < cutoff
502 # Hard masks sequence residues where the corresponding quality score
503 # is below a given cutoff.
504 def mask_seq_hard!(cutoff)
505 raise SeqError, "seq is nil" if self.seq.nil?
506 raise SeqError, "qual is nil" if self.qual.nil?
507 raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
509 na_seq = NArray.to_na(self.seq, "byte")
510 na_qual = NArray.to_na(self.qual, "byte")
511 mask = (na_qual - SCORE_BASE) < cutoff
512 mask *= na_seq.ne("-".ord)
514 na_seq[mask] = 'N'.ord
516 self.seq = na_seq.to_s
521 # Soft masks sequence residues where the corresponding quality score
522 # is below a given cutoff.
523 def mask_seq_soft!(cutoff)
524 raise SeqError, "seq is nil" if self.seq.nil?
525 raise SeqError, "qual is nil" if self.qual.nil?
526 raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
528 na_seq = NArray.to_na(self.seq, "byte")
529 na_qual = NArray.to_na(self.qual, "byte")
530 mask = (na_qual - SCORE_BASE) < cutoff
531 mask *= na_seq.ne("-".ord)
533 na_seq[mask] ^= ' '.ord
535 self.seq = na_seq.to_s
540 # Method that determines if a quality score string can be
541 # absolutely identified as base 33.
543 self.qual.match(/[!-:]/)
546 # Method that determines if a quality score string can be
547 # absolutely identified as base 64.
549 self.qual.match(/[K-h]/)
552 # Method to convert quality scores inbetween formats.
553 # Sanger base 33, range 0-40
554 # 454 base 64, range 0-40
555 # Solexa base 64, range -5-40
556 # Illumina13 base 64, range 0-40
557 # Illumina15 base 64, range 3-40
558 # Illumina18 base 33, range 0-41
559 def convert_scores!(from, to)
561 na_qual = NArray.to_na(self.qual, "byte")
564 when "sanger" then na_qual -= 33
565 when "454" then na_qual -= 64
566 when "solexa" then na_qual -= 64
567 when "illumina13" then na_qual -= 64
568 when "illumina15" then na_qual -= 64
569 when "illumina18" then na_qual -= 33
570 else raise SeqError, "unknown quality score encoding: #{from}"
574 when "sanger" then na_qual += 33
575 when "454" then na_qual += 64
576 when "solexa" then na_qual += 64
577 when "illumina13" then na_qual += 64
578 when "illumina15" then na_qual += 64
579 when "illumina18" then na_qual += 33
580 else raise SeqError, "unknown quality score encoding: #{from}"
583 self.qual = na_qual.to_s
589 # Method to calculate and return the mean quality score.
591 raise SeqError, "Missing qual in entry" if self.qual.nil?
593 na_qual = NArray.to_na(self.qual, "byte")
594 na_qual -= SCORE_BASE
598 # Method to find open reading frames (ORFs).
599 def each_orf(size_min, size_max, start_codons, stop_codons, pick_longest = false)
603 regex_start = Regexp.new(start_codons.join('|'), true)
604 regex_stop = Regexp.new(stop_codons.join('|'), true)
606 while pos_beg and pos_beg < self.length - size_min
607 if pos_beg = self.seq.index(regex_start, pos_beg)
608 if pos_end = self.seq.index(regex_stop, pos_beg)
609 length = (pos_end - pos_beg) + 3
612 if size_min <= length and length <= size_max
613 subseq = self.subseq(pos_beg, length)
615 orfs << [subseq, pos_beg, pos_end + 3]
627 orfs.each { |orf| orf_hash[orf.last] = orf unless orf_hash[orf.last] }
629 orfs = orf_hash.values
633 orfs.each { |orf| yield orf }