use Maasha::KISS;
use Maasha::Biopieces;
use Maasha::Seq;
+use Maasha::BGB::Wiggle;
use vars qw( @ISA @EXPORT );
$beg = $cookie->{ 'NAV_START' };
$end = $cookie->{ 'NAV_END' };
- $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg + 1 );
+ $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg );
$step = 10;
{
# Martin A. Hansen, November 2009.
- # Create a track with features. If there are more than $cookie->FEAT_MAX
- # features the track created will be a histogram, else linear.
-
- my ( $track, # path to kiss file with track data
+ my ( $track, # path to track data
$cookie, # cookie hash
) = @_;
# Returns a list.
- my ( $index, $count, $track_name, $start, $end, $entries, $features );
-
- $start = $cookie->{ 'NAV_START' };
- $end = $cookie->{ 'NAV_END' };
-
- $index = Maasha::KISS::kiss_index_retrieve( "$track/track_data.kiss.json" );
- $count = Maasha::KISS::kiss_index_count( $index, $start, $end );
+ my ( $data_wig, $data_kiss, $track_name, $features );
$track_name = ( split "/", $track )[ -1 ];
$track_name =~ s/^\d+_//;
$track_name =~ s/_/ /g;
- $features = [ {
+ push @{ $features }, {
type => 'text',
txt => $track_name,
font_size => $cookie->{ 'SEQ_FONT_SIZE' },
color => $cookie->{ 'SEQ_COLOR' },
x1 => 0,
y1 => $cookie->{ 'TRACK_OFFSET' },
- } ];
+ };
$cookie->{ 'TRACK_OFFSET' } += 10;
- if ( $count > $cookie->{ 'FEAT_MAX' } )
+ if ( -f "$track/track_data.wig" )
{
-# $entries = Maasha::KISS::kiss_index_get_blocks( $index, $start, $end );
-# push @{ $features }, track_feature_histogram( $cookie, $start, $end, $entries );
- }
+ $data_wig = Maasha::BGB::Wiggle::wiggle_retrieve( "$track/track_data.wig", $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' } );
+
+ push @{ $features }, track_wiggle( $cookie, $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' }, $data_wig );
+ }
+ elsif ( -f "$track/track_data.kiss" )
+ {
+ $data_kiss = Maasha::KISS::kiss_retrieve( "$track/track_data.kiss", $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' } );
+
+ push @{ $features }, track_linear( $cookie, $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' }, $data_kiss );
+ }
else
{
- $entries = Maasha::KISS::kiss_index_get_entries( $index, $start, $end );
- push @{ $features }, track_feature_linear( $cookie, $start, $end, $entries );
- }
+ Maasha::Common::error( "Unknown track data type" );
+ }
return wantarray ? @{ $features } : $features;
}
-sub track_feature_linear
+sub track_wiggle
+{
+ # Martin A. Hansen, February 2010.
+
+ # Create a wiggle track.
+
+ my ( $cookie, # hashref with image draw metrics
+ $beg, # base window beg
+ $end, # base window end
+ $vals, # wiggle values
+ ) = @_;
+
+ # Returns a list.
+
+ my ( $i, $max_val, $min_val, $factor, $factor_height, $x1, $y1, $x2, $y2, $block_max, $mean, @features );
+
+ $cookie->{ 'TRACK_OFFSET' } += 10;
+
+ $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg );
+
+ ( $min_val, $max_val ) = Maasha::Calc::minmax( $vals );
+
+ if ( $max_val == 0 ) {
+ $factor_height = $cookie->{ 'WIGGLE_HEIGHT' } / 1;
+ } else {
+ $factor_height = $cookie->{ 'WIGGLE_HEIGHT' } / $max_val;
+ }
+
+ $block_max = 0;
+
+ $x1 = 0;
+ $y1 = $cookie->{ 'TRACK_OFFSET' } + $cookie->{ 'WIGGLE_HEIGHT' };
+
+ for ( $i = 0; $i < scalar @{ $vals }; $i++ )
+ {
+ $block_max = Maasha::Calc::max( $block_max, $vals->[ $i ] );
+
+ $x2 = int( $i * $factor );
+
+ if ( $x2 > $x1 )
+ {
+ $y2 = $cookie->{ 'TRACK_OFFSET' } + $cookie->{ 'WIGGLE_HEIGHT' } - sprintf( "%.0f", $block_max * $factor_height );
+
+ push @features, {
+ type => 'wiggle',
+ color => $cookie->{ 'FEAT_COLOR' },
+ line_width => 1,
+ x1 => $x1,
+ y1 => $y1,
+ x2 => $x2,
+ y2 => $y2,
+ };
+
+ $x1 = $x2;
+ $y1 = $y2;
+
+ $block_max = 0;
+ }
+ }
+
+ $y2 = $cookie->{ 'TRACK_OFFSET' } + $cookie->{ 'WIGGLE_HEIGHT' };
+
+ push @features, {
+ type => 'wiggle',
+ color => $cookie->{ 'FEAT_COLOR' },
+ line_width => 1,
+ x1 => $x1,
+ y1 => $y1,
+ x2 => $x2,
+ y2 => $y2,
+ };
+
+ unshift @features, {
+ type => 'text',
+ txt => " min: " . Maasha::Calc::commify( $min_val ) . " max: " . Maasha::Calc::commify( $max_val ),
+ font_size => $cookie->{ 'SEQ_FONT_SIZE' } - 2,
+ color => $cookie->{ 'SEQ_COLOR' },
+ x1 => 0,
+ y1 => $cookie->{ 'TRACK_OFFSET' } - 5,
+ };
+
+ $cookie->{ 'TRACK_OFFSET' } += $cookie->{ 'WIGGLE_HEIGHT' } + $cookie->{ 'TRACK_SPACE' };
+
+ return wantarray ? @features : \@features;
+}
+
+
+sub track_linear
{
# Martin A. Hansen, November 2009.
# Returns a list.
- my ( $factor, $entry, $y_step, @ladder, $y_max, $w, $x1, $y1, $x2, $y2, @features );
-
- # @{ $entries } = sort { $a->[ S_BEG ] <=> $b->[ S_BEG ] or $b->[ S_END ] <=> $a->[ S_END ] } @{ $entries };
+ my ( $factor, $entry, $y_step, @ladder, $y_max, $w, $x1, $y1, $x2, $y2, $feature, @features );
- $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg + 1 );
+ $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg );
$y_step = 0;
$y_max = 0;
last if $x1 >= $ladder[ $y_step ] + 1;
}
- $y1 = $cookie->{ 'TRACK_OFFSET' } + ( ( 0.1 + $cookie->{ 'FEAT_WIDTH' } ) * $y_step );
+ $y1 = $cookie->{ 'TRACK_OFFSET' } + ( ( 1.1 + $cookie->{ 'FEAT_WIDTH' } ) * $y_step );
- push @features, {
- type => 'rect',
+ $feature = {
line_width => $cookie->{ 'FEAT_WIDTH' },
color => $cookie->{ 'FEAT_COLOR' },
- title => "Q_ID: $entry->[ Q_ID ] S_BEG: $entry->[ S_BEG ] S_END: $entry->[ S_END ] STRAND: $entry->[ STRAND ]",
+ title => "Q_ID: $entry->[ Q_ID ] S_BEG: $entry->[ S_BEG ] S_END: $entry->[ S_END ]",
q_id => $entry->[ Q_ID ],
s_beg => $entry->[ S_BEG ],
s_end => $entry->[ S_END ],
y2 => $y1 + $cookie->{ 'FEAT_WIDTH' },
};
- $y_max = Maasha::Calc::max( $y_max, $y_step * ( 0.1 + $cookie->{ 'FEAT_WIDTH' } ) );
+ if ( $entry->[ STRAND ] eq '+' or $entry->[ STRAND ] eq '-' ) {
+ $feature->{ 'type' } = 'arrow';
+ } else {
+ $feature->{ 'type' } = 'rect';
+ }
+
+ push @features, $feature;
+
+ $y_max = Maasha::Calc::max( $y_max, $y_step * ( 1.1 + $cookie->{ 'FEAT_WIDTH' } ) );
push @features, feature_align( $entry, $beg, $y1, $factor, $cookie->{ 'FEAT_WIDTH' } ) if $entry->[ ALIGN ] ne '.';
if ( $w >= 1 )
{
- foreach $align ( split /,/, $entry->{ 'ALIGN' } )
+ foreach $align ( split /,/, $entry->[ ALIGN ] )
{
if ( $align =~ /(\d+):([ATCGN-])>([ATCGN-])/ )
{
$hist_height = 100; # pixels
$bucket_width = 5;
$bucket_count = $cookie->{ 'IMG_WIDTH' } / $bucket_width;
- $factor = ( $cookie->{ 'IMG_WIDTH' } / $bucket_width ) / ( $max - $min + 1 );
+ $factor = ( $cookie->{ 'IMG_WIDTH' } / $bucket_width ) / ( $max - $min );
$min_bucket = 999999999;
$max_height = 0;
# Returns a list.
+ my ( $search_track, $search_term, $contig, @tracks, $track, $file, $line, $out_file, $fh, $entry, @entries, $track_name );
+
+ if ( $cookie->{ 'SEARCH' } =~ /^(.+)\s+track:\s*(.+)/i )
+ {
+ $search_term = $1;
+ $search_track = $2;
+
+ $search_track =~ tr/ /_/;
+ }
+ else
+ {
+ $search_term = $cookie->{ 'SEARCH' };
+ }
+
+ foreach $contig ( @{ $cookie->{ 'LIST_CONTIG' } } )
+ {
+ $cookie->{ 'CONTIG' } = $contig;
+
+ push @tracks, path_tracks( $cookie );
+ }
+
+ foreach $track ( @tracks )
+ {
+ if ( $search_track )
+ {
+ $track_name = ( split "/", $track )[ -1 ];
+
+ next if $track_name !~ /$search_track/i;
+ }
+
+ $file = "$track/track_data.kiss";
+
+ if ( -f $file )
+ {
+ $fh = Maasha::Filesys::file_read_open( $file );
+
+ while ( $line = <$fh> )
+ {
+ chomp $line;
+
+ if ( $line =~ /$search_term/i )
+ {
+ $entry = Maasha::KISS::kiss_entry_parse( $line );
+ $entry = Maasha::KISS::kiss2biopiece( $entry );
+ push @entries, $entry;
+ }
+ }
+
+ close $fh;
+ }
+ }
+
+ return wantarray ? @entries : \@entries;
+}
+
+
+sub list_user_dir
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all users directories in the ~/Data/Users
+ # directory with full path.
+
+ # Returns a list.
+
+ my ( @dirs, @users );
+
+ Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+
+ @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users" );
+
+ @users = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+ return wantarray ? @users : \@users;
+}
+
+
+sub list_users
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all users in ~/Data/Users
+
+ # Returns a list.
+
+ my ( @dirs, $dir, @users );
+
+ @dirs = list_user_dir();
+
+ foreach $dir ( @dirs ) {
+ push @users, ( split "/", $dir )[ -1 ];
+ }
+
+ return wantarray ? @users : \@users;
+}
+
+
+sub list_clade_dir
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all clades for a given user in ~/Data/Users
+
+ my ( $user, # user for which to return clades
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @dirs, @clades );
+
+ Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+
+ @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user" );
+
+ @clades = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+ return wantarray ? @clades : \@clades;
+}
+
+
+sub list_clades
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all clades for a given user in ~/Data/Users
+
+ my ( $user, # user for which to return clades
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @dirs, $dir, @clades );
+
+ @dirs = list_clade_dir( $user );
+
+ foreach $dir ( @dirs ) {
+ push @clades, ( split "/", $dir )[ -1 ];
+ }
+
+ return wantarray ? @clades : \@clades;
+}
+
+
+sub list_genome_dir
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all genomes for a given user and clade in ~/Data/Users
+
+ my ( $user, # user for which to return genomes
+ $clade, # clade for which to return genomes
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @dirs, @genomes );
+
+ Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+
+ @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade" );
+
+ @genomes = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+ return wantarray ? @genomes : \@genomes;
+}
+
+
+sub list_genomes
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all genomes for a given user and clade in ~/Data/Users
+
+ my ( $user, # user for which to return genomes
+ $clade, # clade for which to return genomes
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @dirs, $dir, @genomes );
+
+ @dirs = list_genome_dir( $user, $clade );
+
+ foreach $dir ( @dirs ) {
+ push @genomes, ( split "/", $dir )[ -1 ];
+ }
+
+ return wantarray ? @genomes : \@genomes;
+}
+
+
+sub list_assembly_dir
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all assemblies for a given user and clade and genome in ~/Data/Users
+
+ my ( $user, # user for which to return assemblies
+ $clade, # clade for which to return assemblies
+ $genome, # genome for which to return assemblies
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @dirs, @assemblies );
+
+ Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+
+ @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome" );
+
+ @assemblies = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+ return wantarray ? @assemblies : \@assemblies;
+}
+
+
+sub list_assemblies
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all assemblies for a given user and clade and genome in ~/Data/Users
+
+ my ( $user, # user for which to return assemblies
+ $clade, # clade for which to return assemblies
+ $genome, # genome for which to return assemblies
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @dirs, $dir, @assemblies );
+
+ @dirs = list_assembly_dir( $user, $clade, $genome );
+
+ foreach $dir ( @dirs ) {
+ push @assemblies, ( split "/", $dir )[ -1 ];
+ }
+
+ return wantarray ? @assemblies : \@assemblies;
+}
+
+
+sub list_contig_dir
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all assemblies for a given user->clade->genome->assembly in ~/Data/Users
+
+ my ( $user, # user for which to return contigs
+ $clade, # clade for which to return contigs
+ $genome, # genome for which to return contigs
+ $assembly, # assembly for which to return contigs
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @dirs, @contigs );
+
+ Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+
+ @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome/$assembly" );
+
+ @contigs = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+ return wantarray ? @contigs : \@contigs;
+}
+
+
+sub list_contigs
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all contigs for a given user->clade->genome->assembly in ~/Data/Users
+
+ my ( $user, # user for which to return contigs
+ $clade, # clade for which to return contigs
+ $genome, # genome for which to return contigs
+ $assembly, # assembly for which to return contigs
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @dirs, $dir, @contigs );
+
+ @dirs = list_contig_dir( $user, $clade, $genome, $assembly );
+
+ foreach $dir ( @dirs ) {
+ push @contigs, ( split "/", $dir )[ -1 ];
+ }
+
+ return wantarray ? @contigs : \@contigs;
+}
+
+
+sub list_track_dir
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all tracks for a given user->clade->genome->assembly->contig in ~/Data/Users
+
+ my ( $user, # user for which to return tracks
+ $clade, # clade for which to return tracks
+ $genome, # genome for which to return tracks
+ $assembly, # assembly for which to return tracks
+ $contig, # contig for which to return tracks
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @dirs, @tracks );
+
+ Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
+
+ if ( -d "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome/$assembly/$contig/Tracks" ) {
+ @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome/$assembly/$contig/Tracks" );
+ }
+
+ @tracks = grep { $_ !~ /\/\.\.?$/ } @dirs;
+
+ return wantarray ? @tracks : \@tracks;
+}
+
+
+sub list_tracks
+{
+ # Martin A. Hansen, December 2009.
+
+ # List all tracks for a given user->clade->genome->assembly->contig in ~/Data/Users
+
+ my ( $user, # user for which to return tracks
+ $clade, # clade for which to return tracks
+ $genome, # genome for which to return tracks
+ $assembly, # assembly for which to return tracks
+ $contig, # contig for which to return tracks
+ ) = @_;
+
+ # Returns a list.
+
+ my ( @dirs, $dir, @tracks );
+
+ @dirs = list_track_dir( $user, $clade, $genome, $assembly, $contig );
+
+ foreach $dir ( @dirs ) {
+ push @tracks, ( split "/", $dir )[ -1 ];
+ }
+
+ return wantarray ? @tracks : \@tracks;
+}
+
+
+sub max_track
+{
+ # Martin A. Hansen, December 2009.
+
+ # Traverses all contigs for a given user->clade->genome->assembly and
+ # returns the maximum track's prefix value eg. 20 for 20_Genbank.
+
+ my ( $user,
+ $clade,
+ $genome,
+ $assembly
+ ) = @_;
+
+ # Returns an integer
+
+ my ( @contigs, $contig, @tracks, $max );
+
+ @contigs = list_contigs( $user, $clade, $genome, $assembly );
+
+ foreach $contig ( @contigs ) {
+ push @tracks, list_tracks( $user, $clade, $genome, $assembly, $contig );
+ }
+
+ @tracks = sort @tracks;
+
+ if ( scalar @tracks > 0 and $tracks[ -1 ] =~ /^(\d+)/ ) {
+ $max = $1;
+ } else {
+ $max = 0;
+ }
+
+ return $max;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+1;
+
+__END__
+
+
+sub search_tracks_nc
+{
+ # Martin A. Hansen, December 2009.
+
+ # Uses grep to search all tracks in all contigs
+ # for a given pattern and return a list of KISS entries.
+
+ my ( $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
my ( $search_track, $search_term, $contig, @tracks, $track, $file, @features, $track_name, $nc_list );
if ( $cookie->{ 'SEARCH' } =~ /^(.+)\s+track:\s*(.+)/i )
}
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-1;
+sub track_feature
+{
+ # Martin A. Hansen, November 2009.
+
+ # Create a track with features. If there are more than $cookie->FEAT_MAX
+ # features the track created will be a histogram, else linear.
+
+ my ( $track, # path to kiss file with track data
+ $cookie, # cookie hash
+ ) = @_;
+
+ # Returns a list.
+
+ my ( $index, $count, $track_name, $start, $end, $entries, $features );
+
+ $start = $cookie->{ 'NAV_START' };
+ $end = $cookie->{ 'NAV_END' };
+
+ $index = Maasha::KISS::kiss_index_retrieve( "$track/track_data.kiss.index" );
+ $count = Maasha::KISS::kiss_index_count( $index, $start, $end );
+
+ $track_name = ( split "/", $track )[ -1 ];
+ $track_name =~ s/^\d+_//;
+ $track_name =~ s/_/ /g;
+
+ $features = [ {
+ type => 'text',
+ txt => $track_name,
+ font_size => $cookie->{ 'SEQ_FONT_SIZE' },
+ color => $cookie->{ 'SEQ_COLOR' },
+ x1 => 0,
+ y1 => $cookie->{ 'TRACK_OFFSET' },
+ } ];
+ $cookie->{ 'TRACK_OFFSET' } += 10;
+
+ if ( $count > $cookie->{ 'FEAT_MAX' } )
+ {
+ $entries = Maasha::KISS::kiss_index_get_blocks( $index, $start, $end );
+ push @{ $features }, track_feature_histogram( $cookie, $start, $end, $entries );
+ }
+ else
+ {
+ $entries = Maasha::KISS::kiss_index_get_entries( "$track/track_data.kiss", $index, $start, $end );
+ push @{ $features }, track_feature_linear( $cookie, $start, $end, $entries );
+ }
+
+ return wantarray ? @{ $features } : $features;
+}
projects / biopieces.git / blobdiff