changed options in create_blast_db

git-svn-id: http://biopieces.googlecode.com/svn/trunk@690 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/create_blast_db b/bp_bin/create_blast_db
index 8dc857edcfc030f6bde855a3fc80644e59d8af8d..6cbd2bf62d5a031eda9454382419e479ae666b5f 100755 (executable)
--- a/bp_bin/create_blast_db
+++ b/bp_bin/create_blast_db
@@ -36,43 +36,63 @@ use Maasha::Biopieces;
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 
-my ( $options, $in, $out, $record, $fh, $entry, $seq_type, $path );
+my ( $options, $in, $out, $record, $tmp_dir, $file_tmp, $fh_tmp, $entry, $seq_type, $arg );
 
 $options = Maasha::Biopieces::parse_options(
     [
-        { long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
-        { long => 'database',  short => 'd', type => 'file', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'no_stream',  short => 'x', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'directory',  short => 'd', type => 'dir',    mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
     ]   
 );
 
 $in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
 $out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
 
-$path = $options->{ "database" };
-
-$fh = Maasha::Common::write_open( $path );
+$tmp_dir  = Maasha::Biopieces::get_tmpdir();
+$file_tmp = "$tmp_dir/$options->{ 'index_name' }";
+$fh_tmp   = Maasha::Filesys::file_write_open( $file_tmp );
 
 while ( $record = Maasha::Biopieces::get_record( $in ) ) 
 {
-    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
-
     if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
     {
         $seq_type = Maasha::Seq::seq_guess_type( $record->{ 'SEQ' } ) if not $seq_type;
 
-        Maasha::Fasta::put_entry( $entry, $fh );
+        Maasha::Fasta::put_entry( $entry, $fh_tmp );
     }
+
+    Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
 }
 
-close $fh;
+close $fh_tmp;
+
+$arg = "-t $options->{ 'index_name' }";
 
 if ( $seq_type eq "protein" ) {
-    Maasha::Common::run( "formatdb", "-p T -i $path -t $options->{ 'database' } -l /dev/null" );
+    $arg .= " -p T";
 } else {
-    Maasha::Common::run( "formatdb", "-p F -i $path -t $options->{ 'database' } -l /dev/null" );
+    $arg .= " -p F";
 }
 
-unlink $path;
+$arg .= " -i $file_tmp";
+
+if ( $options->{ 'verbose' } )
+{
+    print STDERR "Running: formatdb $arg\n";
+
+    Maasha::Common::run( "formatdb", "$arg" );
+}
+else
+{
+    Maasha::Common::run( "formatdb", "$arg -l /dev/null" );
+}
+
+Maasha::Filesys::dir_create( $options->{ 'directory' } );
+
+unlink $file_tmp;
+
+system( "cp $tmp_dir/* $options->{ 'directory' }" );
 
 Maasha::Biopieces::close_stream( $in );
 Maasha::Biopieces::close_stream( $out );