From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 12 Oct 2011 19:16:27 +0000 (+0000)
Subject: added write_fastq_files
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=b1ad0471346c62ebad82a006d544432668fe280e;p=biopieces.git

added write_fastq_files

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1555 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/write_fastq_files b/bp_bin/write_fastq_files
new file mode 100755
index 0000000..91ba26e
--- /dev/null
+++ b/bp_bin/write_fastq_files
@@ -0,0 +1,69 @@
+#!/usr/bin/env ruby
+
+# Copyright (C) 2007-2011 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Write sequence type records to FASTQ files according to a specified key.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'maasha/fastq'
+require 'pp'
+
+casts = []
+casts << {:long=>'key',       :short=>'k', :type=>'string', :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'dir',       :short=>'d', :type=>'dir!',   :mandatory=>true,  :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'no_stream', :short=>'x', :type=>'flag',   :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+key = options[:key].to_sym
+
+fh_hash = {}
+
+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] and record[key]
+      if fh_hash.has_key? record[key].to_sym
+        fastq_io = fh_hash[record[key].to_sym]
+      else
+        fastq_file = File.join(options[:dir], record[key] + ".fastq")
+        fastq_io   = Fastq.open(fastq_file, "w")
+        fh_hash[record[key].to_sym] = fastq_io
+      end
+
+      fastq_io.puts record
+    end
+
+    output.puts record unless options[:no_stream]
+  end
+end
+
+fh_hash.each_value { |val| val.close }
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__