X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fread_fastq;h=e4fd75f257357988657a205f984a41f356d9eeb4;hb=5de6112b70b59420b245ce636a8b2e3c90acbe00;hp=8aeedf9e1ca52b6fe9ced2334ddee3a12379b4e4;hpb=e1df26dfc188e331d236b08b66b7dfc68e35e5aa;p=biopieces.git

diff --git a/bp_bin/read_fastq b/bp_bin/read_fastq
index 8aeedf9..e4fd75f 100755
--- a/bp_bin/read_fastq
+++ b/bp_bin/read_fastq
@@ -1,6 +1,6 @@
-#!/usr/bin/env perl
+#!/usr/bin/env ruby
 
-# Copyright (C) 2007-2009 Martin A. Hansen.
+# Copyright (C) 2007-2013 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
@@ -18,112 +18,125 @@
 
 # http://www.gnu.org/copyleft/gpl.html
 
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Read FASTQ entries from one or more files.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-use warnings;
-use strict;
-use Maasha::Biopieces;
-use Maasha::Filesys;
-use Maasha::Fastq;
-
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+# This program is part of the Biopieces framework (www.biopieces.org).
 
-my ( $options, $in, $out, $record, $data_in, $num, $entry );
-
-$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 => 'quality', short => 'q', type => 'uint',   mandatory => 'no', default => 20,    allowed => undef, disallowed => undef },
-    ]   
-);
-
-$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-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::Fastq::get_entry( $data_in ) ) 
-    {
-        if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
-        {
-            lowercase_low_scores( $record, $options->{ 'quality' } );
-
-            Maasha::Biopieces::put_record( $record, $out );
-        }
-
-        last if $options->{ "num" } and $num == $options->{ "num" };
-
-        $num++;
-    }
-
-    close $data_in;
-}
-
-Maasha::Biopieces::close_stream( $in );
-Maasha::Biopieces::close_stream( $out );
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-sub lowercase_low_scores
-{
-    # Martin A. Hansen, July 2009.
-
-    # Lowercase residues in sequence that are below a given score threshold.
-
-    # This one would be lovely to have written in C.
-
-    my ( $record,    # Biopiece record
-         $quality,   # quality threshold
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( @seqs, @scores, $i );
-
-    @seqs   = split //, $record->{ 'SEQ' };
-    @scores = split /;/, $record->{ 'SCORES' };
-
-    for ( $i = 0; $i < @scores; $i++ ) {
-        $seqs[ $i ] = lc $seqs[ $i ] if $scores[ $i ] < $quality;
-    }
-
-    $record->{ 'SEQ' }    = join "",  @seqs;
-    $record->{ 'SCORES' } = join ";", @scores;
-}
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+# Read FASTQ entries from one or more files.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-
-BEGIN
-{
-    Maasha::Biopieces::status_set();
-}
-
-
-END
-{
-    Maasha::Biopieces::status_log();
-}
+require 'maasha/biopieces'
+require 'maasha/fastq'
+
+MAX_TEST = 1_000
+
+allowed_enc = 'auto,base_33,base_64'
+
+casts = []
+casts << {:long=>'data_in',  :short=>'i', :type=>'files!', :mandatory=>false, :default=>nil,    :allowed=>nil,         :disallowed=>nil}
+casts << {:long=>'data_in2', :short=>'j', :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=>'encoding', :short=>'e', :type=>'string', :mandatory=>false, :default=>'auto', :allowed=>allowed_enc, :disallowed=>nil}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+encoding = options[:encoding].to_sym
+
+num  = 0
+last = false
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  unless options[:data_in] and options[:data_in].first == '-'
+    input.each_record do |record|
+      output.puts record
+    end
+  end
+
+  if options[:data_in] and options[:data_in2]
+    raise "data_in files differ" if options[:data_in].size != options[:data_in2].size
+
+    (0 ... options[:data_in].size).each do |i|
+      file1 = options[:data_in][i]
+      file2 = options[:data_in2][i]
+
+      io1 = Fastq.open(file1, 'r')
+      io2 = Fastq.open(file2, 'r')
+
+      while entry1 = io1.get_entry and entry2 = io2.get_entry
+        if encoding == :auto
+          if entry1.qual_base33? or entry2.qual_base33?
+            encoding = :base_33
+          elsif entry1.qual_base64? or entry2.qual_base64?
+            encoding = :base_64
+          else
+            raise SeqError, "Could not auto-detect quality score encoding"
+          end
+        end
+
+        entry1.qual_convert!(encoding, :base_33)
+        entry2.qual_convert!(encoding, :base_33)
+        entry1.qual_coerce!(:base_33)
+        entry2.qual_coerce!(:base_33)
+
+        if num < MAX_TEST
+          raise SeqError, "Quality score outside valid range" unless entry1.qual_valid?(:base_33)
+          raise SeqError, "Quality score outside valid range" unless entry2.qual_valid?(:base_33)
+        end
+
+        output.puts entry1.to_bp
+        output.puts entry2.to_bp
+
+        num += 2
+
+        if options[:num] and num >= options[:num]
+          last = true
+          break
+        end
+      end
+
+      io1.close
+      io2.close
+
+      break if last
+    end
+  elsif options[:data_in]
+    options[:data_in].each do |file|
+      Fastq.open(file, 'r') do |fastq|
+        fastq.each do |entry|
+          if encoding == :auto
+            if entry.qual_base33?
+              encoding = :base_33
+            elsif entry.qual_base64?
+              encoding = :base_64
+            else
+              raise SeqError, "Could not auto-detect quality score encoding"
+            end
+          end
+
+          entry.qual_convert!(encoding, :base_33)
+          entry.qual_coerce!(:base_33)
+
+          if num < MAX_TEST
+            raise SeqError, "Quality score outside valid range" unless entry.qual_valid?(:base_33)
+          end
+
+          output.puts entry.to_bp
+          num += 1
+
+          if options[:num] == num
+            last = true
+            break
+          end
+        end
+      end
+
+      break if last
+    end
+  end
+end
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<