require 'maasha/align'
require 'maasha/usearch'
+class Seq
+ ALPH_DNA = %w{A T C G}
+ ALPH_AMBI = %w{A T C G M R W S Y K V H D B N}
+
+ BIT_INDEL = 0
+ BIT_A = 1 << 0
+ BIT_T = 1 << 1
+ BIT_C = 1 << 2
+ BIT_G = 1 << 3
+
+ BIT_M = BIT_A | BIT_C
+ BIT_R = BIT_A | BIT_G
+ BIT_W = BIT_A | BIT_T
+ BIT_S = BIT_C | BIT_G
+ BIT_Y = BIT_C | BIT_T
+ BIT_K = BIT_G | BIT_T
+ BIT_V = BIT_A | BIT_C | BIT_G
+ BIT_H = BIT_A | BIT_C | BIT_T
+ BIT_D = BIT_A | BIT_G | BIT_T
+ BIT_B = BIT_C | BIT_G | BIT_T
+ BIT_N = BIT_G | BIT_A | BIT_T | BIT_C
+
+ BITMAP = [
+ BIT_A,
+ BIT_T,
+ BIT_C,
+ BIT_G,
+ BIT_M,
+ BIT_R,
+ BIT_W,
+ BIT_S,
+ BIT_Y,
+ BIT_K,
+ BIT_V,
+ BIT_H,
+ BIT_D,
+ BIT_B,
+ BIT_N
+ ]
+
+ TR_NUC = "-" + ALPH_AMBI.join("").downcase
+ TR_HEX = [BIT_INDEL].pack("C") + BITMAP.pack("C*")
+
+ def to_na
+ entry = Seq.new
+ entry.seq = NArray.to_na(self.seq.downcase.tr(TR_NUC, TR_HEX), "byte")
+ entry.qual = NArray.to_na(self.qual, "byte") - Seq::SCORE_BASE if self.qual
+ entry
+ end
+end
+
+class Align
+ def to_na
+ cols = self.length
+ rows = self.members
+
+ na_seq = NArray.byte(cols, rows)
+ na_qual = NArray.byte(cols, rows)
+
+ self.entries.each_with_index do |entry, i|
+ na_entry = entry.to_na
+ na_seq[true, i] = na_entry.seq
+ na_qual[true, i] = na_entry.qual
+ end
+
+ return na_seq, na_qual
+ end
+end
+
+class Denoise
+ attr_reader :align
+
+ ROW_A = 0
+ ROW_T = 1
+ ROW_C = 2
+ ROW_G = 3
+
+ def initialize(align, options)
+ @align = align
+ @options = options
+ @cols = align.length
+ @rows = align.members
+ @na_seq, @na_qual = align.to_na
+ @na_rescored = nil
+ end
+
+ def denoise_sequences
+ freq = NArray.int(@cols, 4)
+
+ freq[true, ROW_A] = (@na_seq & Seq::BIT_A > 0).to_type("int").sum(1)
+ freq[true, ROW_T] = (@na_seq & Seq::BIT_T > 0).to_type("int").sum(1)
+ freq[true, ROW_C] = (@na_seq & Seq::BIT_C > 0).to_type("int").sum(1)
+ freq[true, ROW_G] = (@na_seq & Seq::BIT_G > 0).to_type("int").sum(1)
+
+ mask_freq = freq.eq freq.max(1)
+
+ mask_freq[true, ROW_A] *= Seq::BIT_A
+ mask_freq[true, ROW_T] *= Seq::BIT_T
+ mask_freq[true, ROW_C] *= Seq::BIT_C
+ mask_freq[true, ROW_G] *= Seq::BIT_G
+
+ mask_replace = mask_freq.max(1)
+
+ mask_bad = @na_qual <= @options[:quality_min]
+
+ @na_rescored = mask_bad.dup
+
+ new_values = mask_replace * mask_bad
+ old_values = mask_bad.eq(0) * @na_seq
+
+ old_scores = @na_qual * mask_bad.eq(0)
+
+ sum = old_scores.to_type("float").sum(1)
+ count = (old_scores > 0).to_type("int").sum(1)
+ mean = (sum / count).to_type("byte")
+
+ new_scores = mask_bad * mean
+
+ @na_seq = new_values + old_values
+ @na_qual = new_scores + old_scores
+
+ self
+ end
+
+ # Method that lowercase residues that have been removed during
+ # the determination of the consensus sequence.
+ def mask_sequences
+ @align.each_with_index do |entry, i|
+ entry.qual = (@na_qual[true, i] + Seq::SCORE_BASE).to_s
+
+ j = 0
+
+ while entry.seq[j] do
+ if @na_rescored[j, i] == 0
+ entry.seq[j] = entry.seq[j].upcase
+ else
+ entry.seq[j] = entry.seq[j].downcase
+ end
+
+ j += 1
+ end
+ end
+ end
+end
+
casts = []
casts << {:long=>'cluster_ident', :short=>'i', :type=>'float', :mandatory=>true, :default=>0.97, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'cluster_min', :short=>'c', :type=>'uint', :mandatory=>true, :default=>1, :allowed=>nil, :disallowed=>"0"}
casts << {:long=>'sequence_min', :short=>'s', :type=>'uint', :mandatory=>true, :default=>1, :allowed=>nil, :disallowed=>"0"}
casts << {:long=>'residue_min', :short=>'r', :type=>'float', :mandatory=>true, :default=>0.3, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'gap_max', :short=>'g', :type=>'float', :mandatory=>true, :default=>0.4, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'quality_min', :short=>'q', :type=>'uint', :mandatory=>true, :default=>10, :allowed=>nil, :disallowed=>nil}
casts << {:long=>'quality_mean', :short=>'Q', :type=>'uint', :mandatory=>true, :default=>15, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'cpus', :short=>'C', :type=>'uint', :mandatory=>true, :default=>1, :allowed=>nil, :disallowed=>"0"}
options = Biopieces.options_parse(ARGV, casts)
tmpdir = Biopieces.mktmpdir
fasta_file_align = File.join(tmpdir, "test.aln.fna")
options[:identity] = options[:cluster_ident]
+options[:msa] = true
def alignment_to_fastq(entries, index)
entries.each do |entry|
- cluster, ident, name = entry.seq_name.split('|')
+ seq_name = entry.seq_name.sub(/^\*/, '')
+ elem = index.get(seq_name) # disk based lookup
- entry.qual = index.get(name).qual # disk based lookup
+ entry.seq_name = elem.seq_name
+ entry.qual = elem.qual
entry.seq.scan(/-+/) do |m|
- entry.qual = entry.qual[0 ... $`.length] + ('@' * m.length) + entry.qual[$`.length .. -1]
+ entry.qual = entry.qual[0 ... $`.length] + ('!' * m.length) + entry.qual[$`.length .. -1]
end
end
end
input.each_record do |record|
if record[:SEQ] and record[:SCORES]
entry = Seq.new_bp(record)
+ orig_name = entry.seq_name.dup
entry.seq_name = seq_count.to_s
fasta_io.puts entry.to_fasta
fastq_io.puts entry.to_fastq
- index.add(entry)
+ index.add(entry, orig_name)
seq_count += 1
else
fastq_io = File.open(fastq_file, "r")
index.ios = fastq_io
- tot_clusters = 0
- tot_entries = 0
-
uc = Usearch.new(fasta_file, fasta_file_align, options)
- uc.sort_length
- uc.cluster
- uc.ustar
+ uc.sortbylength
+ uc.cluster_smallmem
uc.each_alignment do |align|
- if align.members >= options[:cluster_min]
- align.options = options
-
- alignment_to_fastq(align.entries, index)
-
- cons = align.consensus
- cons.seq_name = "#{tot_clusters}_#{align.members}"
- cons.indels_remove
-
- new_record = cons.to_bp
- new_record[:CLUSTER] = tot_clusters
- new_record[:CLUSTER_COUNT] = align.members
-
- puts align if options[:verbose]
-
- output.puts new_record
-
- tot_clusters += 1
+ align.options = options
+ alignment_to_fastq(align.entries, index)
+
+ dn = Denoise.new(align, options)
+ dn.denoise_sequences
+ dn.mask_sequences
+
+ if options[:verbose]
+ puts dn.align
+ else
+ dn.align.each do |entry|
+ output.puts entry.to_bp
+ end
end
end
end
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-__END__
projects / biopieces.git / commitdiff