# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-# Write Biopiece records to the KISS Genome browser.
+# Write Biopiece records to the Biopieces Genome browser.
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
use Maasha::KISS;
use Maasha::Biopieces;
use Maasha::Fasta;
+use Maasha::BGB::Track;
+use Maasha::BGB::Wiggle;
use Maasha::Filesys;
use constant {
SEQ_NAME => 0,
SEQ => 1,
+
+ S_ID => 0,
};
# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-my ( $data_dir, $user, $options, $path, $in, $out, $tmp_dir, %fh_hash, $fh_out, $record, $entry, $key, @dirs, $dir, $dst_dir, @nums, $num, $contig_dir );
+my ( $data_dir, $user, $options, $path, $in, $out, $tmp_dir, %fh_hash, $fh_out, $record, $entry, $key, $dst_dir, @nums, $num, $contig_dir, $wig );
-$data_dir = Maasha::Biopieces::biopiecesrc( "KISS_DATA_DIR" );
-$user = Maasha::Biopieces::biopiecesrc( "KISS_USER" );
+$data_dir = Maasha::Biopieces::biopiecesrc( "BGB_DATA_DIR" );
+$user = Maasha::Biopieces::biopiecesrc( "BGB_USER" );
$options = Maasha::Biopieces::parse_options(
[
- { long => 'user', short => 'u', type => 'string', mandatory => 'no', default => $user, allowed => undef, disallowed => undef },
- { long => 'clade', short => 'c', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
- { 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 },
+ { long => 'user', short => 'u', type => 'string', mandatory => 'no', default => $user, allowed => undef, disallowed => undef },
+ { long => 'clade', short => 'c', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+ { 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 => 'track_type', short => 'T', type => 'string', mandatory => 'no', default => 'linear', allowed => 'linear,wiggle', 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 },
]
);
{
$options->{ 'track_name' } =~ tr/ /_/;
- $path = join "/", $data_dir, "Users/", $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' };
+ $path = join "/", $data_dir, "Users", $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' };
Maasha::Common::error( qq(Path not found: "$path") ) if not -d $path;
{
if ( $entry = Maasha::KISS::biopiece2kiss( $record ) )
{
- $entry->{ 'S_ID' } = ( split / /, $entry->{ 'S_ID' } )[ 0 ];
+ $entry->[ S_ID ] = ( split / /, $entry->[ S_ID ] )[ 0 ];
- if ( not exists $fh_hash{ $entry->{ 'S_ID' } } ) {
- $fh_hash{ $entry->{ 'S_ID' } } = Maasha::Filesys::file_write_open( "$tmp_dir/$entry->{ 'S_ID' }" );
+ if ( not exists $fh_hash{ $entry->[ S_ID ] } ) {
+ $fh_hash{ $entry->[ S_ID ] } = Maasha::Filesys::file_write_open( "$tmp_dir/$entry->[ S_ID ]" );
}
- $fh_out = $fh_hash{ $entry->{ 'S_ID' } };
+ $fh_out = $fh_hash{ $entry->[ S_ID ] };
Maasha::KISS::kiss_entry_put( $entry, $fh_out );
}
Maasha::Biopieces::put_record( $record, $out ) if not $options->{ "no_stream" };
}
+ $num = Maasha::BGB::Track::max_track( $options->{ 'user' }, $options->{ 'clade' }, $options->{ 'genome' }, $options->{ 'assembly' } );
+ $num = sprintf( "%04d", $num + 10 );
+
foreach $key ( keys %fh_hash )
{
close $fh_hash{ $key };
$dst_dir = Maasha::Filesys::dir_create_if_not_exists( "$path/$key" );
$dst_dir = Maasha::Filesys::dir_create_if_not_exists( "$dst_dir/Tracks" );
- @dirs = Maasha::Filesys::ls_dirs( $dst_dir );
-
- foreach $dir ( @dirs )
- {
- $dir = ( split "/", $dir )[ -1 ];
-
- if ( $dir =~ /^(\d+)/ ) {
- push @nums, $1;
- }
- }
-
- @nums = sort { $a <=> $b } @nums;
-
- $num = $nums[ -1 ] || 0;
-
- $num += 10;
-
$dst_dir = "$dst_dir/$num" . "_$options->{ 'track_name' }";
Maasha::Filesys::dir_create( $dst_dir );
- Maasha::Filesys::file_copy( "$tmp_dir/$key", "$dst_dir/track_data.kiss" );
+ if ( $options->{ 'track_type' } eq 'linear' )
+ {
+ Maasha::Filesys::file_copy( "$tmp_dir/$key", "$dst_dir/track_data.kiss" );
- Maasha::KISS::kiss_sort( "$dst_dir/track_data.kiss" );
- Maasha::KISS::kiss_index( "$dst_dir/track_data.kiss" );
+ Maasha::KISS::kiss_sort( "$dst_dir/track_data.kiss" );
+ }
+ elsif ( $options->{ 'track_type' } eq 'wiggle' )
+ {
+ $wig = Maasha::BGB::Wiggle::wiggle_encode( "$tmp_dir/$key" );
+ Maasha::BGB::Wiggle::wiggle_store( "$dst_dir/track_data.wig", $wig );
+ }
unlink "$tmp_dir/$key";
}
Maasha::Common::error( qq(Path not found: "$path") ) if not -d $path;
- $dst_dir = Maasha::Filesys::dir_create( "$path/$options->{ 'genome' }" );
+ $dst_dir = Maasha::Filesys::dir_create_if_not_exists( "$path/$options->{ 'genome' }" );
$dst_dir = Maasha::Filesys::dir_create( "$dst_dir/$options->{ 'assembly' }" );
while ( $record = Maasha::Biopieces::get_record( $in ) )