-#!/usr/bin/env perl
+#!/usr/bin/env ruby
-# Copyright (C) 2007-2009 Martin A. Hansen.
+# Copyright (C) 2007-2010 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-# Analyze sequences in the stream.
-
-
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+# This program is part of the Biopieces framework (www.biopieces.org).
-use warnings;
-use strict;
-use Maasha::Biopieces;
-use Maasha::Common;
-use Maasha::Seq;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my ( $options, $in, $out, $record, $analysis );
-
-$options = Maasha::Biopieces::parse_options();
-
-$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-while ( $record = Maasha::Biopieces::get_record( $in ) )
-{
- seq_analyze( $record ) if $record->{ "SEQ" };
-
- Maasha::Biopieces::put_record( $record, $out );
-}
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+# Analyze sequences in the stream.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-sub seq_analyze
-{
- # Martin A. Hansen, July 2009.
+require 'maasha/biopieces'
+require 'maasha/seq'
- # Analyzes the composition of the string in the record and appends
- # the analysis to the record.
+casts = []
- my ( $record, # Biopiece record with a SEQ entry.
- ) = @_;
-
- # Returns nothing.
-
- my ( %char_hash, @indels, @alph, $char, $gc, $at, $lc, $max, $indels );
-
- %char_hash = Maasha::Common::str_analyze( $record->{ 'SEQ' } );
-
- $record->{ 'SEQ_TYPE' } = Maasha::Seq::seq_guess_type( $record->{ 'SEQ' } );
- $record->{ 'SEQ_LEN' } = length $record->{ 'SEQ' };
-
- @alph = Maasha::Seq::seq_alph( $record->{ 'SEQ_TYPE' } . "_AMBI" );
- @indels = qw( - ~ . _ );
-
- $max = 0;
-
- foreach $char ( @alph )
- {
- $char_hash{ $char } += $char_hash{ lc $char } || 0;
-
- $record->{ "RES[$char]" } = $char_hash{ $char };
-
- $max = $char_hash{ $char } if $char_hash{ $char } > $max;
-
- $record->{ "RES_SUM" } += $char_hash{ $char };
- }
-
- $indels = 0;
-
- map { $record->{ "RES[$_]" } = $char_hash{ $_ }; $indels += $char_hash{ $_ } } @indels;
-
- if ( $record->{ "SEQ_TYPE" } =~ /DNA|RNA/i )
- {
- $gc = $char_hash{ "G" } + $char_hash{ "C" };
- $at = $char_hash{ "A" } + $char_hash{ "T" } + $char_hash{ "U" };
-
- $lc = 0;
-
- map { $lc += $char_hash{ lc $_ } || 0 } @alph;
-
- $record->{ "MIX_INDEX" } = sprintf( "%.2f", $max / ( $record->{ "SEQ_LEN" } - $indels ) );
- $record->{ "GC%" } = sprintf( "%.2f", 100 * $gc / ( $record->{ "SEQ_LEN" } - $indels ) );
- $record->{ "SOFT_MASK%" } = sprintf( "%.2f", 100 * $lc / ( $record->{ "SEQ_LEN" } - $indels ) );
- $record->{ "HARD_MASK%" } = sprintf( "%.2f", 100 * ( $char_hash{ "n" } + $char_hash{ "N" } ) / ( $record->{ "SEQ_LEN" } - $indels ) );
- $record->{ "MELT_TEMP" } = sprintf( "%.2f", 4 * $gc + 2 * $at );
- }
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+options = Biopieces.options_parse(ARGV, casts)
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ if record[:SEQ]
+ seq = Seq.new(record[:SEQ_NAME], record[:SEQ], record[:SEQ_TYPE], record[:SCORE])
+ comp = seq.composition
-BEGIN
-{
- Maasha::Biopieces::status_set();
-}
+ comp.each_pair do |key,val|
+ record["RES[#{key}]"] = val
+ end
+ record["SOFT_MASK%"] = seq.soft_mask
+ record["HARD_MASK%"] = (comp["N"].to_f / (seq.len - seq.indels).to_f * 100.0).round(2)
+ record["GC%"] = ((comp["G"] + comp["C"]).to_f / (seq.len - seq.indels).to_f * 100.0).round(2)
+ end
-END
-{
- Maasha::Biopieces::status_log();
-}
+ output.puts record
+ end
+end
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<