changed layout of ruby source

[biopieces.git] / code_ruby / lib / maasha / fasta.rb

diff --git a/code_ruby/lib/maasha/fasta.rb b/code_ruby/lib/maasha/fasta.rb
new file mode 100644 (file)
index 0000000..f57a622
--- /dev/null
+++ b/code_ruby/lib/maasha/fasta.rb
@@ -0,0 +1,65 @@
+# 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 software is part of the Biopieces framework (www.biopieces.org).
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+require 'maasha/seq'
+require 'maasha/filesys'
+
+# Error class for all exceptions to do with FASTA.
+class FastaError < StandardError; end
+
+class Fasta < Filesys
+  # Method to get the next FASTA entry form an ios and return this
+  # as a Seq object. If no entry is found or eof then nil is returned.
+  def get_entry
+    block = @io.gets($/ + '>')
+    return nil if block.nil?
+
+    block.chomp!($/ + '>')
+
+    (seq_name, seq) = block.split($/, 2)
+
+    raise FastaError, "Bad FASTA format" if seq_name.nil? or seq.nil?
+
+    entry          = Seq.new
+    entry.type     = @type.nil? ? nil : @type.downcase
+    entry.seq      = seq.gsub(/\s/, '')
+    entry.seq_name = seq_name.sub(/^>/, '').rstrip
+
+    raise FastaError, "Bad FASTA format" if entry.seq_name.empty?
+    raise FastaError, "Bad FASTA format" if entry.seq.empty?
+
+    entry
+  end
+
+  # TODO - this should be some custom to_s method instead.
+  def puts(record)
+    if record.has_key? :SEQ_NAME and record.has_key? :SEQ
+      @io.print ">#{record[:SEQ_NAME]}\n"
+      @io.print "#{record[:SEQ]}\n"
+    end
+  end
+end
+
+
+__END__