X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fread_sam;h=1da5ff58535aef7be08647dcb7a13942aa99a111;hb=48bea5c28b89dc5586d0bddb338ccd6ba23aa1f9;hp=4096c922e68c768676c038be9f58232d5dfe16c9;hpb=e911e9fe83302e5bcd051bac5a212c3c72c92f63;p=biopieces.git

diff --git a/bp_bin/read_sam b/bp_bin/read_sam
index 4096c92..1da5ff5 100755
--- a/bp_bin/read_sam
+++ b/bp_bin/read_sam
@@ -1,6 +1,6 @@
-#!/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
@@ -18,77 +18,51 @@
 
 # http://www.gnu.org/copyleft/gpl.html
 
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Read SAM entries from one or more files.
-
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+# This program is part of the Biopieces framework (www.biopieces.org).
 
-use warnings;
-use strict;
-use Maasha::Biopieces;
-use Maasha::Filesys;
-use Maasha::SAM;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-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' },
-    ]   
-);
-
-$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::SAM::sam_entry_get( $data_in ) ) 
-    {
-        if ( $record = Maasha::SAM::sam2biopiece( $entry ) ) {
-            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 );
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
+# Read SAM entries from one or more files.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-
-BEGIN
-{
-    Maasha::Biopieces::status_set();
-}
-
-
-END
-{
-    Maasha::Biopieces::status_log();
-}
+require 'maasha/biopieces'
+require 'maasha/sam'
+
+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'}
+
+options = Biopieces.options_parse(ARGV, casts)
+
+num  = 0
+last = false
+
+Biopieces.open(options[:stream_in], options[:stream_out]) do |input, output|
+  input.each_record do |record|
+    output.puts record
+  end
+
+  if options[:data_in]
+    options[:data_in].each do |file|
+      Sam.open(file, 'r') do |sam|
+        sam.each do |entry|
+          output.puts Sam.to_bp(entry)
+          num += 1
+
+          if options[:num] and options[:num] == num
+            last = true
+            break
+          end
+        end
+      end
+
+      break if last
+    end
+  end
+end
 
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<