assemble_pairs revamp

git-svn-id: http://biopieces.googlecode.com/svn/trunk@2145 74ccb610-7750-0410-82ae-013aeee3265d

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

diff --git a/bp_bin/assemble_pairs2 b/bp_bin/assemble_pairs2
deleted file mode 100755 (executable)
index 66c2a7b..0000000
--- a/bp_bin/assemble_pairs2
+++ /dev/null
@@ -1,119 +0,0 @@
-#!/usr/bin/env ruby
-
-# Copyright (C) 2007-2013 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# This program is part of the Biopieces framework (www.biopieces.org).
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Assemble ordered overlapping pair-end sequences in the stream.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-require 'maasha/biopieces'
-require 'maasha/seq'
-require 'maasha/seq/assemble'
-require 'pp'
-
-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
-
-  if entry2.seq_name =~ /^([^ ]+) \d:/
-    name2 = $1
-  elsif entry2.seq_name =~ /^(.+)\/\d$/
-    name2 = $1
-  else
-    raise "Could not match sequence name: #{entry2.seq_name}"
-  end
-
-  name1 == name2
-end
-
-casts = []
-casts << {:long=>'mismatches',  :short=>'m', :type=>'uint', :mandatory=>false, :default=>5,   :allowed=>nil, :disallowed=>nil}
-casts << {:long=>'overlap_min', :short=>'o', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}
-casts << {:long=>'overlap_max', :short=>'p', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>"0"}
-
-options = Biopieces.options_parse(ARGV, casts)
-
-entry1 = nil
-entry2 = nil
-
-Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
-  input.each_record do |record|
-    if record[:SEQ_NAME] and record[:SEQ] and record[:SCORES]
-      if entry1.nil?
-        entry1 = Seq.new_bp(record)
-      elsif entry2.nil?
-        entry2 = Seq.new_bp(record)
-      end
-
-      if entry1 and
-         entry2 and
-         entry1.length >= options[:overlap_min] and
-         entry2.length >= options[:overlap_min]
-
-        if names_match(entry1, entry2)
-          entry2.type = :dna
-          entry2.reverse!.complement!
-
-          merged = Assemble.pair(
-            entry1,
-            entry2,
-            mismatches_max:options[:mismatches],
-            overlap_min:options[:overlap_min],
-            overlap_max:options[:overlap_max]
-          )
-
-          if merged
-            new_record = merged.to_bp
-
-            if merged.seq_name =~ /overlap=(\d+):hamming=(\d+)$/
-              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
-    else
-      output.puts record
-    end
-  end
-end
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__