{ long => 'genome', short => 'g', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
{ long => 'assembly', short => 'a', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
{ long => 'track_name', short => 't', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+ { long => 'force', short => 'f', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
{ long => 'no_stream', short => 'x', type => 'flag', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
]
);
if ( $entry = Maasha::Fasta::biopiece2fasta( $record ) )
{
$entry->[ SEQ_NAME ] = ( split " ", $entry->[ SEQ_NAME ] )[ 0 ];
+
+ if ( $options->{ 'force' } ) {
+ Maasha::Filesys::dir_remove( "$dst_dir/$entry->[ SEQ_NAME ]" );
+ }
+
$contig_dir = Maasha::Filesys::dir_create( "$dst_dir/$entry->[ SEQ_NAME ]" );
$contig_dir = Maasha::Filesys::dir_create( "$contig_dir/Sequence" );
use warnings;
use strict;
use Maasha::Biopieces;
-use Maasha::KISS::IO;
+use Maasha::KISS;
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
while ( $record = Maasha::Biopieces::get_record( $in ) )
{
- if ( $entry = Maasha::KISS::IO::biopiece2kiss( $record ) ) {
- Maasha::KISS::IO::kiss_entry_put( $entry, $fh );
+ if ( $entry = Maasha::KISS::biopiece2kiss( $record ) ) {
+ Maasha::KISS::kiss_entry_put( $entry, $fh );
}
Maasha::Biopieces::put_record( $record, $out ) if not $options->{ 'no_stream' };