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 :Hamming, 'maasha/seq/hamming'
34 autoload :Levenshtein, 'maasha/seq/levenshtein'
35 autoload :Ambiguity, 'maasha/seq/ambiguity'
40 PROTEIN = %w[f l s y c w p h q r i m t n k v a d e g]
43 # Translation table 11
44 # (http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG11)
45 # AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
46 # Starts = ---M---------------M------------MMMM---------------M------------
47 # Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
48 # Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
49 # Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
51 "TTG" => "M", "CTG" => "M", "ATT" => "M", "ATC" => "M",
52 "ATA" => "M", "ATG" => "M", "GTG" => "M"
56 "TTT" => "F", "TCT" => "S", "TAT" => "Y", "TGT" => "C",
57 "TTC" => "F", "TCC" => "S", "TAC" => "Y", "TGC" => "C",
58 "TTA" => "L", "TCA" => "S", "TAA" => "*", "TGA" => "*",
59 "TTG" => "L", "TCG" => "S", "TAG" => "*", "TGG" => "W",
60 "CTT" => "L", "CCT" => "P", "CAT" => "H", "CGT" => "R",
61 "CTC" => "L", "CCC" => "P", "CAC" => "H", "CGC" => "R",
62 "CTA" => "L", "CCA" => "P", "CAA" => "Q", "CGA" => "R",
63 "CTG" => "L", "CCG" => "P", "CAG" => "Q", "CGG" => "R",
64 "ATT" => "I", "ACT" => "T", "AAT" => "N", "AGT" => "S",
65 "ATC" => "I", "ACC" => "T", "AAC" => "N", "AGC" => "S",
66 "ATA" => "I", "ACA" => "T", "AAA" => "K", "AGA" => "R",
67 "ATG" => "M", "ACG" => "T", "AAG" => "K", "AGG" => "R",
68 "GTT" => "V", "GCT" => "A", "GAT" => "D", "GGT" => "G",
69 "GTC" => "V", "GCC" => "A", "GAC" => "D", "GGC" => "G",
70 "GTA" => "V", "GCA" => "A", "GAA" => "E", "GGA" => "G",
71 "GTG" => "V", "GCG" => "A", "GAG" => "E", "GGG" => "G"
74 # Error class for all exceptions to do with Seq.
75 class SeqError < StandardError; end
78 # Quality scores bases
86 attr_accessor :seq_name, :seq, :type, :qual
88 # Class method to instantiate a new Sequence object given
90 def self.new_bp(record)
91 seq_name = record[:SEQ_NAME]
93 type = record[:SEQ_TYPE].to_sym if record[:SEQ_TYPE]
94 qual = record[:SCORES]
96 self.new(seq_name, seq, type, qual)
99 # Class method that generates all possible oligos of a specifed length and type.
100 def self.generate_oligos(length, type)
101 raise SeqError, "Cannot generate negative oligo length: #{length}" if length <= 0
104 when :dna then alph = DNA
105 when :rna then alph = RNA
106 when :protein then alph = PROTEIN
108 raise SeqError, "Unknown sequence type: #{type}"
113 (1 .. length).each do
116 oligos.each do |oligo|
128 # Initialize a sequence object with the following arguments:
129 # - seq_name: Name of the sequence.
130 # - seq: The sequence.
131 # - type: The sequence type - DNA, RNA, or protein
132 # - qual: An Illumina type quality scores string.
133 def initialize(seq_name = nil, seq = nil, type = nil, qual = nil)
140 # Method that guesses and returns the sequence type
141 # by inspecting the first 100 residues.
143 raise SeqError, "Guess failed: sequence is nil" if self.seq.nil?
145 case self.seq[0 ... 100].downcase
146 when /[flpqie]/ then return :protein
147 when /[u]/ then return :rna
152 # Method that guesses and sets the sequence type
153 # by inspecting the first 100 residues.
155 self.type = self.type_guess
159 # Returns the length of a sequence.
161 self.seq.nil? ? 0 : self.seq.length
166 # Return the number indels in a sequence.
168 regex = Regexp.new(/[#{Regexp.escape(INDELS.join(""))}]/)
169 self.seq.scan(regex).size
172 # Method to remove indels from seq and qual if qual.
175 self.seq.delete!(Regexp.escape(INDELS.join('')))
177 na_seq = NArray.to_na(self.seq, "byte")
178 na_qual = NArray.to_na(self.qual, "byte")
179 mask = NArray.byte(self.length)
182 mask += na_seq.eq(c.ord)
187 self.seq = na_seq[mask].to_s
188 self.qual = na_qual[mask].to_s
194 # Method that returns true is a given sequence type is DNA.
199 # Method that returns true is a given sequence type is RNA.
204 # Method that returns true is a given sequence type is protein.
206 self.type == :protein
209 # Method to transcribe DNA to RNA.
211 raise SeqError, "Cannot transcribe 0 length sequence" if self.length == 0
212 raise SeqError, "Cannot transcribe sequence type: #{self.type}" unless self.is_dna?
214 self.seq.tr!('Tt','Uu')
217 # Method to reverse-transcribe RNA to DNA.
219 raise SeqError, "Cannot reverse-transcribe 0 length sequence" if self.length == 0
220 raise SeqError, "Cannot reverse-transcribe sequence type: #{self.type}" unless self.is_rna?
222 self.seq.tr!('Uu','Tt')
225 # Method to translate a DNA sequence to protein.
226 def translate!(trans_tab = 11)
227 raise SeqError, "Sequence type must be 'dna' - not #{self.type}" unless self.type == :dna
228 raise SeqError, "Sequence length must be a multiplum of 3 - was: #{self.length}" unless (self.length % 3) == 0
232 codon_start_hash = TRANS_TAB11_START
233 codon_hash = TRANS_TAB11
235 raise SeqError, "Unknown translation table: #{trans_tab}"
238 codon = self.seq[0 ... 3].upcase
240 aa = codon_start_hash[codon]
242 raise SeqError, "Unknown start codon: #{codon}" if aa.nil?
248 while i < self.length
249 codon = self.seq[i ... i + 3].upcase
251 aa = codon_hash[codon]
253 raise SeqError, "Unknown codon: #{codon}" if aa.nil?
267 alias :to_protein! :translate!
269 def translate(trans_tab = 11)
270 self.dup.translate!(trans_tab)
273 alias :to_protein :translate
275 # Method that given a Seq entry returns a Biopieces record (a hash).
277 raise SeqError, "Missing seq_name" if self.seq_name.nil?
278 raise SeqError, "Missing seq" if self.seq.nil?
281 record[:SEQ_NAME] = self.seq_name
282 record[:SEQ] = self.seq
283 record[:SEQ_LEN] = self.length
284 record[:SCORES] = self.qual if self.qual
288 # Method that given a Seq entry returns a FASTA entry (a string).
289 def to_fasta(wrap = nil)
290 raise SeqError, "Missing seq_name" if self.seq_name.nil? or self.seq_name == ''
291 raise SeqError, "Missing seq" if self.seq.nil? or self.seq.empty?
293 seq_name = self.seq_name.to_s
297 seq.gsub!(/(.{#{wrap}})/) do |match|
304 ">" + seq_name + $/ + seq + $/
307 # Method that given a Seq entry returns a FASTQ entry (a string).
309 raise SeqError, "Missing seq_name" if self.seq_name.nil?
310 raise SeqError, "Missing seq" if self.seq.nil?
311 raise SeqError, "Missing qual" if self.qual.nil?
313 seq_name = self.seq_name.to_s
315 qual = self.qual.to_s
317 "@" + seq_name + $/ + seq + $/ + "+" + $/ + qual + $/
320 # Method that generates a unique key for a
321 # DNA sequence and return this key as a Fixnum.
325 self.seq.upcase.each_char do |char|
329 when 'A' then key |= 0
330 when 'C' then key |= 1
331 when 'G' then key |= 2
332 when 'T' then key |= 3
333 else raise SeqError, "Bad residue: #{char}"
340 # Method to reverse the sequence.
342 Seq.new(self.seq_name, self.seq.reverse, self.type, self.qual ? self.qual.reverse : self.qual)
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 entry.seq_name = self.seq_name
358 entry.type = self.type
359 entry.qual = self.qual
362 entry.seq = self.seq.tr('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
364 entry.seq = self.seq.tr('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn')
366 raise SeqError, "Cannot complement sequence type: #{self.type}"
372 # Method that complements sequence including ambiguity codes.
374 raise SeqError, "Cannot complement 0 length sequence" if self.length == 0
377 self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'TCGAAYRWSKMDHBVNtcgaayrwskmdhbvn')
379 self.seq.tr!('AGCUTRYWSMKHDVBNagcutrywsmkhdvbn', 'UCGAAYRWSKMDHBVNucgaayrwskmdhbvn')
381 raise SeqError, "Cannot complement sequence type: #{self.type}"
387 # Method to determine the Hamming Distance between
388 # two Sequence objects (case insensitive).
389 def hamming_distance(entry, options = nil)
390 if options and options[:ambiguity]
391 Hamming.distance(self.seq, entry.seq)
393 self.seq.upcase.hamming_distance(entry.seq.upcase)
397 # Method to determine the Edit Distance between
398 # two Sequence objects (case insensitive).
399 def edit_distance(entry)
400 Levenshtein.distance(self.seq, entry.seq)
403 # Method that generates a random sequence of a given length and type.
404 def generate(length, type)
405 raise SeqError, "Cannot generate sequence length < 1: #{length}" if length <= 0
408 when :dna then alph = DNA
409 when :rna then alph = RNA
410 when :protein then alph = PROTEIN
412 raise SeqError, "Unknown sequence type: #{type}"
415 seq_new = Array.new(length) { alph[rand(alph.size)] }.join("")
421 # Method to return a new Seq object with shuffled sequence.
423 Seq.new(self.seq_name, self.seq.split('').shuffle!.join, self.type, self.qual)
426 # Method to shuffle a sequence randomly inline.
428 self.seq = self.seq.split('').shuffle!.join
432 # Method to add two Seq objects.
434 new_entry = Seq.new()
435 new_entry.seq = self.seq + entry.seq
436 new_entry.type = self.type if self.type == entry.type
437 new_entry.qual = self.qual + entry.qual if self.qual and entry.qual
441 # Method to concatenate sequence entries.
443 raise SeqError, "sequences of different types" unless self.type == entry.type
444 raise SeqError, "qual is missing in one entry" unless self.qual.class == entry.qual.class
446 self.seq << entry.seq
447 self.qual << entry.qual unless entry.qual.nil?
452 # Index method for Seq objects.
455 entry.seq_name = self.seq_name
456 entry.seq = self.seq[*args]
457 entry.type = self.type
458 entry.qual = self.qual[*args] unless self.qual.nil?
463 # Index assignment method for Seq objects.
464 def []=(*args, entry)
465 self.seq[*args] = entry.seq[*args]
466 self.qual[*args] = entry.qual[*args] unless self.qual.nil?
471 # Method that returns a subsequence of from a given start position
472 # and of a given length.
473 def subseq(start, length = self.length - start)
474 raise SeqError, "subsequence start: #{start} < 0" if start < 0
475 raise SeqError, "subsequence length: #{length} < 0" if length < 0
476 raise SeqError, "subsequence start + length > Seq.length: #{start} + #{length} > #{self.length}" if start + length > self.length
480 qual = "" unless self.qual.nil?
482 stop = start + length - 1
484 seq = self.seq[start .. stop]
485 qual = self.qual[start .. stop] unless self.qual.nil?
488 seq_name = self.seq_name.nil? ? nil : self.seq_name.dup
490 Seq.new(seq_name, seq, self.type, qual)
493 # Method that replaces a sequence with a subsequence from a given start position
494 # and of a given length.
495 def subseq!(start, length = self.length - start)
496 s = subseq(start, length)
498 self.seq_name = s.seq_name
506 # Method that returns a subsequence of a given length
507 # beginning at a random position.
508 def subseq_rand(length)
509 if self.length - length + 1 == 0
512 start = rand(self.length - length + 1)
515 self.subseq(start, length)
518 # Method that returns the residue compositions of a sequence in
519 # a hash where the key is the residue and the value is the residue
524 self.seq.upcase.each_char do |char|
531 # Method that returns the percentage of hard masked residues
532 # or N's in a sequence.
534 ((self.seq.upcase.scan("N").size.to_f / (self.len - self.indels).to_f) * 100).round(2)
537 # Method that returns the percentage of soft masked residues
538 # or lower cased residues in a sequence.
540 ((self.seq.scan(/[a-z]/).size.to_f / (self.len - self.indels).to_f) * 100).round(2)
543 # Hard masks sequence residues where the corresponding quality score
544 # is below a given cutoff.
545 def mask_seq_hard!(cutoff)
546 raise SeqError, "seq is nil" if self.seq.nil?
547 raise SeqError, "qual is nil" if self.qual.nil?
548 raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
550 na_seq = NArray.to_na(self.seq, "byte")
551 na_qual = NArray.to_na(self.qual, "byte")
552 mask = (na_qual - SCORE_BASE) < cutoff
553 mask *= na_seq.ne("-".ord)
555 na_seq[mask] = 'N'.ord
557 self.seq = na_seq.to_s
562 # Soft masks sequence residues where the corresponding quality score
563 # is below a given cutoff.
564 def mask_seq_soft!(cutoff)
565 raise SeqError, "seq is nil" if self.seq.nil?
566 raise SeqError, "qual is nil" if self.qual.nil?
567 raise SeqError, "cufoff value: #{cutoff} out of range #{SCORE_MIN} .. #{SCORE_MAX}" unless (SCORE_MIN .. SCORE_MAX).include? cutoff
569 na_seq = NArray.to_na(self.seq, "byte")
570 na_qual = NArray.to_na(self.qual, "byte")
571 mask = (na_qual - SCORE_BASE) < cutoff
572 mask *= na_seq.ne("-".ord)
574 na_seq[mask] ^= ' '.ord
576 self.seq = na_seq.to_s
581 # Method that determines if a quality score string can be
582 # absolutely identified as base 33.
584 self.qual.match(/[!-:]/) ? true : false
587 # Method that determines if a quality score string may be base 64.
589 self.qual.match(/[K-h]/) ? true : false
592 # Method to determine if a quality score is valid accepting only 0-40 range.
593 def qual_valid?(encoding)
594 raise SeqError, "Missing qual" if self.qual.nil?
597 when :base_33 then return true if self.qual.match(/^[!-I]*$/)
598 when :base_64 then return true if self.qual.match(/^[@-h]*$/)
599 else raise SeqError, "unknown quality score encoding: #{encoding}"
605 # Method to coerce quality scores to be within the 0-40 range.
606 def qual_coerce!(encoding)
607 raise SeqError, "Missing qual" if self.qual.nil?
610 when :base_33 then self.qual.tr!("[J-~]", "I")
611 when :base_64 then self.qual.tr!("[i-~]", "h")
612 else raise SeqError, "unknown quality score encoding: #{encoding}"
618 # Method to convert quality scores.
619 def qual_convert!(from, to)
620 raise SeqError, "unknown quality score encoding: #{from}" unless from == :base_33 or from == :base_64
621 raise SeqError, "unknown quality score encoding: #{to}" unless to == :base_33 or to == :base_64
623 if from == :base_33 and to == :base_64
624 na_qual = NArray.to_na(self.qual, "byte")
626 self.qual = na_qual.to_s
627 elsif from == :base_64 and to == :base_33
628 self.qual.tr!("[;-?]", "@") # Handle negative Solexa values from -5 to -1 (set these to 0).
629 na_qual = NArray.to_na(self.qual, "byte")
631 self.qual = na_qual.to_s
637 # Method to calculate and return the mean quality score.
639 raise SeqError, "Missing qual in entry" if self.qual.nil?
641 na_qual = NArray.to_na(self.qual, "byte")
642 na_qual -= SCORE_BASE
647 # Method to find open reading frames (ORFs).
648 def each_orf(size_min, size_max, start_codons, stop_codons, pick_longest = false)
652 regex_start = Regexp.new(start_codons.join('|'), true)
653 regex_stop = Regexp.new(stop_codons.join('|'), true)
655 while pos_beg and pos_beg < self.length - size_min
656 if pos_beg = self.seq.index(regex_start, pos_beg)
657 if pos_end = self.seq.index(regex_stop, pos_beg)
658 length = (pos_end - pos_beg) + 3
661 if size_min <= length and length <= size_max
662 subseq = self.subseq(pos_beg, length)
664 orfs << [subseq, pos_beg, pos_end + 3]
676 orfs.each { |orf| orf_hash[orf.last] = orf unless orf_hash[orf.last] }
678 orfs = orf_hash.values
682 orfs.each { |orf| yield orf }