adding bzip2 support in ruby

[biopieces.git] / bp_bin / denoise_seq

diff --git a/bp_bin/denoise_seq b/bp_bin/denoise_seq
index ff557b431a6d6d57d152c5e7f69dd8202fbd60a6..baa62ad7eb6102e724f7ad7b02d842ceb9d2d2d3 100755 (executable)
--- a/bp_bin/denoise_seq
+++ b/bp_bin/denoise_seq
@@ -37,8 +37,13 @@ require 'maasha/align'
 require 'maasha/usearch'
 
 casts = []
-casts << {:long=>'identity',    :short=>'i', :type=>'float', :mandatory=>true, :default=>0.97, :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'cluster_min', :short=>'c', :type=>'uint',  :mandatory=>true, :default=>2,    :allowed=>nil, :disallowed=>"0"}
+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}
 
 options          = Biopieces.options_parse(ARGV, casts)
 tmpdir           = Biopieces.mktmpdir
@@ -46,6 +51,8 @@ fastq_file       = File.join(tmpdir, "test.fq")
 fasta_file       = File.join(tmpdir, "test.fna")
 fasta_file_align = File.join(tmpdir, "test.aln.fna")
 
+options[:identity] = options[:cluster_ident]
+
 def alignment_to_fastq(entries, index)
   entries.each do |entry|
     cluster, ident, name = entry.seq_name.split('|')
@@ -65,7 +72,7 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   Fasta.open(fasta_file, "w") do |fasta_io|
     Fastq.open(fastq_file, "w") do |fastq_io|
       input.each_record do |record|
-        if record.has_key? :SEQ and record.has_key? :SCORES
+        if record[:SEQ] and record[:SCORES]
           entry = Seq.new_bp(record)
           entry.seq_name = seq_count.to_s
 
@@ -95,6 +102,8 @@ Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
 
   uc.each_alignment do |align|
     if align.members >= options[:cluster_min]
+      align.options = options
+
       alignment_to_fastq(align.entries, index)
 
       cons          = align.consensus