# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $default, $formats, $options, $in, $out, $record, $file_tmp, $fh_tmp, $type, $entry );
+my ( $default, $formats, $options, $in, $out, $record, $tmp_dir, $file_tmp, $fh_tmp, $type, $entry );
$options = Maasha::Biopieces::parse_options(
[
{ long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
{ long => 'index_name', short => 'i', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
- { long => 'prefix_length', short => 'p', type => 'uint', mandatory => 'no', default => undef, allowed => undef, disallowed => 0 },
]
);
$in = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-$file_tmp = $options->{ 'index_name' };
+$tmp_dir = Maasha::Biopieces::get_tmpdir();
+$file_tmp = "$tmp_dir/create_vmatch_index.seq";
$fh_tmp = Maasha::Filesys::file_write_open( $file_tmp );
while ( $record = Maasha::Biopieces::get_record( $in ) )
close $fh_tmp;
-if ( $type eq "protein" ) {
- Maasha::Common::run( "mkvtree", "-db $file_tmp -protein -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
+if ( $options->{ 'verbose' } ) {
+ Maasha::Common::run( "mkvtree", "-db $file_tmp -" . ( lc $type ) . " -pl -allout -indexname $options->{ 'index_name' }" );
} else {
- Maasha::Common::run( "mkvtree", "-db $file_tmp -dna -pl $options->{ 'prefix_length' } -allout -indexname $file_tmp > /dev/null 2>&1" );
+ Maasha::Common::run( "mkvtree", "-db $file_tmp -" . ( lc $type ) . " -pl -allout -indexname $options->{ 'index_name' } > /dev/null 2>&1" );
}
unlink $file_tmp;
+Maasha::Filesys::dir_remove( $tmp_dir );
Maasha::Biopieces::close_stream( $in );
Maasha::Biopieces::close_stream( $out );