assemble_pairs revamp

[biopieces.git] / bp_bin / assemble_pairs

diff --git a/bp_bin/assemble_pairs b/bp_bin/assemble_pairs
index c9e0eb09c2b3eebe8fa58c8f32bfa0f426b17f47..66c2a7bd68015572df1cb530746e539005027cce 100755 (executable)
--- a/bp_bin/assemble_pairs
+++ b/bp_bin/assemble_pairs
@@ -29,82 +29,85 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'maasha/biopieces'
-require 'maasha/fastq'
+require 'maasha/seq'
+require 'maasha/seq/assemble'
 require 'pp'
 
-casts = []
-casts << {:long=>'overlap', :short=>'o', :type=>'uint', :mandatory=>false, :default=>1, :allowed=>nil, :disallowed=>"0"}
+def names_match(entry1, entry2)
+  if entry1.seq_name =~ /^([^ ]+) \d:/
+    name1 = $1
+  elsif entry1.seq_name =~ /^(.+)\/\d$/
+    name1 = $1
+  else
+    raise "Could not match sequence name: #{entry1.seq_name}"
+  end
 
-options = Biopieces.options_parse(ARGV, casts)
+  if entry2.seq_name =~ /^([^ ]+) \d:/
+    name2 = $1
+  elsif entry2.seq_name =~ /^(.+)\/\d$/
+    name2 = $1
+  else
+    raise "Could not match sequence name: #{entry2.seq_name}"
+  end
 
-tmpdir   = Biopieces.mktmpdir
-file_in1 = File.join(tmpdir, "in1.fq")
-file_in2 = File.join(tmpdir, "in2.fq")
-file_out = File.join(tmpdir, "out.fq")
+  name1 == name2
+end
 
-io_in1 = Fastq.open(file_in1, 'w')
-io_in2 = Fastq.open(file_in2, 'w')
+casts = []
+casts << {:long=>'mismatches',  :short=>'m', :type=>'uint', :mandatory=>false, :default=>5,   :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'overlap_min', :short=>'o', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}
+casts << {:long=>'overlap_max', :short=>'p', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}
+
+options = Biopieces.options_parse(ARGV, casts)
 
-name1  = ""
-name2  = ""
-entry1 = ""
-entry2 = ""
+entry1 = nil
+entry2 = nil
 
 Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
   input.each_record do |record|
     if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
-      entry = Seq.new_bp(record)
-
-      case entry.seq_name
-      when /^(.+)\/(\d)$/   # Illumina 1.5
-        name = $1
-        pair = $2.to_i
-        type = 15
-      when /^(.+) (\d):/    # Illumina 1.8
-        name = $1
-        pair = $2.to_i
-        type = 18
-      else
-        $stderr.puts "WARNING: Unmatched sequence name: #{entry.seq_name}"
-      end
-
-      if pair == 1
-        name1  = name.dup
-        entry1 = entry.dup
-      else
-        name2  = name.dup
-        entry2 = entry.dup
+      if entry1.nil?
+        entry1 = Seq.new_bp(record)
+      elsif entry2.nil?
+        entry2 = Seq.new_bp(record)
       end
 
-      if name1 != nil and name1 == name2
-        io_in1.puts entry1.to_fastq
-        io_in2.puts entry2.to_fastq
+      if entry1 and
+         entry2 and
+         entry1.length >= options[:overlap_min] and
+         entry2.length >= options[:overlap_min]
+
+        if names_match(entry1, entry2)
+          entry2.type = :dna
+          entry2.reverse!.complement!
+
+          merged = Assemble.pair(
+            entry1,
+            entry2,
+            mismatches_max:options[:mismatches],
+            overlap_min:options[:overlap_min],
+            overlap_max:options[:overlap_max]
+          )
+
+          if merged
+            new_record = merged.to_bp
+
+            if merged.seq_name =~ /overlap=(\d+):hamming=(\d+)$/
+              new_record[:OVERLAP_LEN]  = $1
+              new_record[:HAMMING_DIST] = $2
+            end
+
+            output.puts new_record
+          end
+        else
+          raise "name mismatch: #{entry1.seq_name} != #{entry2.seq_name}"
+        end
+
+        entry1 = nil
+        entry2 = nil
       end
-    end
-  end
-
-  io_in1.close
-  io_in2.close
-
-  cmd = "pandaseq"
-  cmd << " -F"
-  cmd << " -B"
-  cmd << " -N"
-  cmd << " -o #{options[:overlap]}"
-  cmd << " -f #{file_in1}"
-  cmd << " -r #{file_in2}"
-  cmd << " > #{file_out}"
-  cmd << " 2> /dev/null" unless options[:verbose]
-
-  $stderr.puts cmd if options[:verbose]
-
-  system(cmd)
-
-  raise RunTimeError "Error: command failed: #{cmd}" unless $?.success?
-
-  Fastq.open(file_out) do |ios|
-    ios.each do |entry|
-      output.puts entry.to_bp
+    else
+      output.puts record
     end
   end
 end