# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
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
+++ /dev/null
-#!/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__