refactoring of assemble_pairs

[biopieces.git] / bp_bin / write_fasta

diff --git a/bp_bin/write_fasta b/bp_bin/write_fasta
index fdf5bd287f78613d2aea83bb9b15f855cad57e77..f44d6f4fb64d2188b83cda14d2da7e29e68c2cbe 100755 (executable)
--- a/bp_bin/write_fasta
+++ b/bp_bin/write_fasta
@@ -1,6 +1,66 @@
-#!/usr/bin/env perl
+#!/usr/bin/env ruby
 
-use warnings;
-use strict;
+# Copyright (C) 2007-2012 Martin A. Hansen.
 
-use Maasha::BioRun;
+# 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 sequences from stream in FASTA format.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/biopieces'
+require 'maasha/fasta'
+
+casts = []
+casts << {long: 'no_stream', short: 'x', type: 'flag',   mandatory: false, default: nil, allowed: nil,               disallowed: nil}
+casts << {long: 'data_out',  short: 'o', type: 'file',   mandatory: false, default: nil, allowed: nil,               disallowed: nil}
+casts << {long: 'wrap',      short: 'w', type: 'uint',   mandatory: false, default: nil, allowed: nil,               disallowed: "0"}
+casts << {long: 'compress',  short: 'Z', type: 'string', mandatory: false, default: nil, allowed: "gzip,bzip,bzip2", disallowed: nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+compress = options[:compress] ? options[:compress].to_sym : nil
+
+raise "--data_out is mandatory for compressed output" if compress and not options[:data_out]
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  fasta_out = options[:data_out] ? Fasta.open(options[:data_out], 'w', compress: compress) : STDOUT
+
+  input.each do |record|
+    if record[:SEQ_NAME] and record[:SEQ]
+      entry = Seq.new_bp(record)
+
+      fasta_out.puts entry.to_fasta(options[:wrap])
+    end
+
+    output.puts record unless options[:no_stream]
+  end
+
+  fasta_out.close
+end
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__