-#!/usr/bin/env perl -w
+#!/usr/bin/env ruby
-# Copyright (C) 2007-2009 Martin A. Hansen.
+# 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
# http://www.gnu.org/copyleft/gpl.html
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Read EMBL entries from one or more files.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-use strict;
-use Maasha::Biopieces;
-use Maasha::Filesys;
-use Maasha::EMBL;
-
-
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+# This program is part of the Biopieces framework (www.biopieces.org).
-my ( $options, $in, $out, %options2, $file, $data_in, $num, $entry, $record );
-
-$options = Maasha::Biopieces::parse_options(
- [
- { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'num', short => 'n', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
- { long => 'keys', short => 'k', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'feats', short => 'f', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- { long => 'quals', short => 'q', type => 'list', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
- ]
-);
-
-$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-map { $options2{ "keys" }{ $_ } = 1 } @{ $options->{ "keys" } };
-map { $options2{ "feats" }{ $_ } = 1 } @{ $options->{ "feats" } };
-map { $options2{ "quals" }{ $_ } = 1 } @{ $options->{ "quals" } };
-
-while ( $record = Maasha::Biopieces::get_record( $in ) ) {
- Maasha::Biopieces::put_record( $record, $out );
-}
-
-if ( $options->{ 'data_in' } )
-{
- $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
-
- $num = 1;
-
- while ( $entry = Maasha::EMBL::get_embl_entry( $data_in ) )
- {
- $record = Maasha::EMBL::parse_embl_entry( $entry, \%options2 );
-
- my ( $feat, $feat2, $qual, $qual_val, $record_copy );
-
- $record_copy = dclone $record;
-
- delete $record_copy->{ "FT" };
-
- Maasha::Biopieces::put_record( $record_copy, $out );
-
- delete $record_copy->{ "SEQ" };
-
- foreach $feat ( keys %{ $record->{ "FT" } } )
- {
- $record_copy->{ "FEAT_TYPE" } = $feat;
-
- foreach $feat2 ( @{ $record->{ "FT" }->{ $feat } } )
- {
- foreach $qual ( keys %{ $feat2 } )
- {
- $qual_val = join "; ", @{ $feat2->{ $qual } };
-
- $qual =~ s/^_//;
- $qual = uc $qual;
-
- $record_copy->{ $qual } = $qual_val;
- }
-
- Maasha::Biopieces::put_record( $record_copy, $out );
- }
- }
-
- last if $options->{ "num" } and $num == $options->{ "num" };
-
- $num++;
- }
-
- close $data_in;
-}
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+# Read EMBL entries from one or more files.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-BEGIN
-{
- $run_time_beg = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::log_biopiece();
-}
-
-END
-{
- Maasha::Biopieces::close_stream( $in );
- Maasha::Biopieces::close_stream( $out );
-
- $run_time_end = Maasha::Biopieces::run_time();
-
- Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
-}
+require 'maasha/biopieces'
+require 'maasha/embl'
+
+casts = []
+casts << {:long=>'data_in', :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'num', :short=>'n', :type=>'uint', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'keys', :short=>'k', :type=>'list', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'features', :short=>'f', :type=>'list', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+casts << {:long=>'qualifiers', :short=>'q', :type=>'list', :mandatory=>false, :default=>nil, :allowed=>nil, :disallowed=>nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+hash_keys = options[:keys].inject(Hash.new) { |h,k| h[k.upcase.to_sym] = true; h } if options[:keys]
+hash_feats = options[:features].inject(Hash.new) { |h,k| h[k.upcase.to_sym] = true; h } if options[:features]
+hash_quals = options[:qualifiers].inject(Hash.new) { |h,k| h[k.upcase.to_sym] = true; h } if options[:qualifiers]
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ output.puts record
+ end
+
+ num = 0
+ last = false
+
+ if options[:data_in]
+ options[:data_in].each do |file|
+ EMBL.open(file, 'r') do |embl_io|
+ embl_io.each(hash_keys, hash_feats, hash_quals) do |entry|
+ output.puts entry
+
+ num += 1
+
+ if options[:num] and options[:num] == num
+ last = true
+ break
+ end
+ end
+ end
+
+ break if last
+ end
+ end
+end
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<