-#!/usr/bin/env perl
+#!/usr/bin/env ruby
-# Copyright (C) 2007-2010 Martin A. Hansen.
+# Copyright (C) 2007-2012 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Trim sequence ends for residues with a low quality score.
-
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+# This program is part of the Biopieces framework (www.biopieces.org).
-use warnings;
-use strict;
-use Maasha::Biopieces;
-use Maasha::Fastq;
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+# Trim sequence ends removing residues with a low quality score.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+require 'maasha/biopieces'
+require 'maasha/seq'
+require 'pp'
-my ( $options, $in, $out, $record, $left, $right, $pos_l, $pos_r );
-
-$options = Maasha::Biopieces::parse_options(
- [
- { long => 'min', short => 'm', type => 'uint', mandatory => 'no', default => 15, allowed => undef, disallowed => 0 },
- { long => 'trim', short => 't', type => 'string', mandatory => 'no', default => 'both', allowed => 'left,right,both', disallowed => undef },
- ]
-);
-
-$right = 1 if $options->{ 'trim' } eq 'right';
-$left = 1 if $options->{ 'trim' } eq 'left';
-$right = 1 if $options->{ 'trim' } eq 'both';
-$left = 1 if $options->{ 'trim' } eq 'both';
-
-$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+casts = []
+casts << {:long=>'min_qual', :short=>'m', :type=>'uint', :mandatory=>true, :default=>20, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'min_len', :short=>'l', :type=>'uint', :mandatory=>true, :default=>3, :allowed=>nil, :disallowed=>'0'}
+casts << {:long=>'trim', :short=>'t', :type=>'string', :mandatory=>true, :default=>'both', :allowed=>'left,right,both', :disallowed=>nil}
-while ( $record = Maasha::Biopieces::get_record( $in ) )
-{
- if ( exists $record->{ 'SEQ' } and exists $record->{ 'SCORES' } )
- {
- if ( $right )
- {
- $pos_r = Maasha::Fastq::trim_right( $record->{ 'SCORES' }, $options->{ 'min' } );
-
- $record->{ 'SEQ' } = substr $record->{ 'SEQ' }, 0, $pos_r + 1;
- $record->{ 'SCORES' } = substr $record->{ 'SCORES' }, 0, $pos_r + 1;
- $record->{ 'TRIM_RIGHT' } = $pos_r;
- }
-
- if ( $left )
- {
- $pos_l = Maasha::Fastq::trim_left( $record->{ 'SCORES' }, $options->{ 'min' } );
-
- $record->{ 'SEQ' } = substr $record->{ 'SEQ' }, $pos_l;
- $record->{ 'SCORES' } = substr $record->{ 'SCORES' }, $pos_l;
- $record->{ 'TRIM_LEFT' } = $pos_l;
- }
-
- $record->{ 'SEQ_LEN' } = length $record->{ 'SEQ' };
- }
-
- Maasha::Biopieces::put_record( $record, $out );
-}
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+options = Biopieces.options_parse(ARGV, casts)
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+ input.each_record do |record|
+ if record.has_key? :SEQ and record.has_key? :SCORES
+ entry = Seq.new_bp(record)
-BEGIN
-{
- Maasha::Biopieces::status_set();
-}
+ case options[:trim]
+ when /both/ then entry.quality_trim!(options[:min_qual], options[:min_len])
+ when /left/ then entry.quality_trim_left!(options[:min_qual], options[:min_len])
+ when /right/ then entry.quality_trim_right!(options[:min_qual], options[:min_len])
+ end
+ record.merge! entry.to_bp
+ end
-END
-{
- Maasha::Biopieces::status_log();
-}
+ output.puts record
+ end
+end
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<