1 package Maasha::BGB::Track;
3 # Copyright (C) 2009 Martin A. Hansen.
5 # This program is free software; you can redistribute it and/or
6 # modify it under the terms of the GNU General Public License
7 # as published by the Free Software Foundation; either version 2
8 # of the License, or (at your option) any later version.
10 # This program is distributed in the hope that it will be useful,
11 # but WITHOUT ANY WARRANTY; without even the implied warranty of
12 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 # GNU General Public License for more details.
15 # You should have received a copy of the GNU General Public License
16 # along with this program; if not, write to the Free Software
17 # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
19 # http://www.gnu.org/copyleft/gpl.html
22 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
25 # Routines for creating Biopieces Browser tracks.
28 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
38 use Maasha::Biopieces;
40 use Maasha::BGB::Wiggle;
42 use vars qw( @ISA @EXPORT );
44 @ISA = qw( Exporter );
61 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
66 # Martin A. Hansen, November 2009.
68 # Create a track with a ruler of tics and positions for
71 my ( $cookie, # browser cookie
76 my ( $beg, $end, $factor, $step, $i, $txt, $x, @ruler );
78 $beg = $cookie->{ 'NAV_START' };
79 $end = $cookie->{ 'NAV_END' };
80 $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg );
84 while ( ( $end - $beg ) / $step > 20 ) {
88 for ( $i = $beg; $i < $end; $i++ )
90 if ( ( $i % $step ) == 0 )
92 $txt = "|" . Maasha::Calc::commify( $i );
93 $x = sprintf( "%.0f", ( ( $i - $beg ) * $factor ) + 2 );
95 if ( $x > 0 and $x + ( $cookie->{ 'RULER_FONT_SIZE' } * length $txt ) < $cookie->{ 'IMG_WIDTH' } )
100 font_size => $cookie->{ 'RULER_FONT_SIZE' },
101 color => $cookie->{ 'RULER_COLOR' },
103 y1 => $cookie->{ 'TRACK_OFFSET' },
109 $cookie->{ 'TRACK_OFFSET' } += $cookie->{ 'TRACK_SPACE' };
111 return wantarray ? @ruler : \@ruler;
117 # Martin A. Hansen, November 2009.
119 # Create a sequence track by extracting the appropriate
120 # stretch of sequence from the sequence file.
122 my ( $cookie, # browser cookie
127 my ( $file, $fh, $seq, @chars, $factor, $x_offset, $i, @seq_list );
129 if ( $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' } + 1 <= 220 ) # only add sequence if less than or equal to 220.
131 $file = path_seq( $cookie );
132 $fh = Maasha::Filesys::file_read_open( $file );
133 $seq = Maasha::Filesys::file_read( $fh, $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' } + 1 );
136 @chars = split //, $seq;
138 $factor = $cookie->{ 'IMG_WIDTH' } / @chars;
140 $x_offset = sprintf( "%.0f", ( $factor / 2 ) - ( $cookie->{ 'SEQ_FONT_SIZE' } / 2 ) );
141 $x_offset = 0 if $x_offset < 0;
143 for ( $i = 0; $i < @chars; $i++ )
148 font_size => $cookie->{ 'SEQ_FONT_SIZE' },
149 color => $cookie->{ 'SEQ_COLOR' },
150 x1 => sprintf( "%.0f", $x_offset + $i * $factor ),
151 y1 => $cookie->{ 'TRACK_OFFSET' },
155 $cookie->{ 'TRACK_OFFSET' } += $cookie->{ 'TRACK_SPACE' };
157 return wantarray ? @seq_list : \@seq_list;
168 # Martin A. Hansen, November 2009.
170 my ( $track, # path to track data
171 $cookie, # cookie hash
176 my ( $data_wig, $data_kiss, $track_name, $features );
178 $track_name = ( split "/", $track )[ -1 ];
179 $track_name =~ s/^\d+_//;
180 $track_name =~ s/_/ /g;
182 push @{ $features }, {
185 font_size => $cookie->{ 'SEQ_FONT_SIZE' },
186 color => $cookie->{ 'SEQ_COLOR' },
188 y1 => $cookie->{ 'TRACK_OFFSET' },
191 $cookie->{ 'TRACK_OFFSET' } += 10;
193 if ( -f "$track/track_data.wig" )
195 $data_wig = Maasha::BGB::Wiggle::wiggle_retrieve( "$track/track_data.wig", $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' } );
197 push @{ $features }, track_wiggle( $cookie, $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' }, $data_wig );
199 elsif ( -f "$track/track_data.kiss" )
201 $data_kiss = Maasha::KISS::kiss_retrieve( "$track/track_data.kiss", $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' } );
203 push @{ $features }, track_linear( $cookie, $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' }, $data_kiss );
207 Maasha::Common::error( "Unknown track data type" );
210 return wantarray ? @{ $features } : $features;
216 # Martin A. Hansen, February 2010.
218 # Create a wiggle track.
220 my ( $cookie, # hashref with image draw metrics
221 $beg, # base window beg
222 $end, # base window end
223 $vals, # wiggle values
228 my ( $i, $max_val, $min_val, $factor, $factor_height, $x1, $y1, $x2, $y2, $block_max, $mean, @features );
230 $cookie->{ 'TRACK_OFFSET' } += 10;
232 $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg );
234 ( $min_val, $max_val ) = Maasha::Calc::minmax( $vals );
236 if ( $max_val == 0 ) {
237 $factor_height = $cookie->{ 'WIGGLE_HEIGHT' } / 1;
239 $factor_height = $cookie->{ 'WIGGLE_HEIGHT' } / $max_val;
245 $y1 = $cookie->{ 'TRACK_OFFSET' } + $cookie->{ 'WIGGLE_HEIGHT' };
247 for ( $i = 0; $i < scalar @{ $vals }; $i++ )
249 $block_max = Maasha::Calc::max( $block_max, $vals->[ $i ] );
251 $x2 = int( $i * $factor );
255 $y2 = $cookie->{ 'TRACK_OFFSET' } + $cookie->{ 'WIGGLE_HEIGHT' } - sprintf( "%.0f", $block_max * $factor_height );
259 color => $cookie->{ 'FEAT_COLOR' },
274 $y2 = $cookie->{ 'TRACK_OFFSET' } + $cookie->{ 'WIGGLE_HEIGHT' };
278 color => $cookie->{ 'FEAT_COLOR' },
288 txt => " min: " . Maasha::Calc::commify( $min_val ) . " max: " . Maasha::Calc::commify( $max_val ),
289 font_size => $cookie->{ 'SEQ_FONT_SIZE' } - 2,
290 color => $cookie->{ 'SEQ_COLOR' },
292 y1 => $cookie->{ 'TRACK_OFFSET' } - 5,
295 $cookie->{ 'TRACK_OFFSET' } += $cookie->{ 'WIGGLE_HEIGHT' } + $cookie->{ 'TRACK_SPACE' };
297 return wantarray ? @features : \@features;
303 # Martin A. Hansen, November 2009.
305 # Create a linear feature track where the granularity depends
306 # on the lenght of the features and the browser window width.
308 my ( $cookie, # hashref with image draw metrics
309 $beg, # base window beg
310 $end, # base window end
311 $entries, # list of unsorted KISS entries
316 my ( $factor, $entry, $y_step, @ladder, $y_max, $w, $x1, $y1, $x2, $y2, $feature, @features );
318 $factor = $cookie->{ 'IMG_WIDTH' } / ( $end - $beg );
322 foreach $entry ( @{ $entries } )
324 $w = sprintf( "%.0f", ( $entry->[ S_END ] - $entry->[ S_BEG ] + 1 ) * $factor );
328 $x1 = sprintf( "%.0f", ( $entry->[ S_BEG ] - $beg ) * $factor );
330 for ( $y_step = 0; $y_step < @ladder; $y_step++ ) {
331 last if $x1 >= $ladder[ $y_step ] + 1;
334 $y1 = $cookie->{ 'TRACK_OFFSET' } + ( ( 1.1 + $cookie->{ 'FEAT_WIDTH' } ) * $y_step );
337 line_width => $cookie->{ 'FEAT_WIDTH' },
338 color => $cookie->{ 'FEAT_COLOR' },
339 title => "Q_ID: $entry->[ Q_ID ] S_BEG: $entry->[ S_BEG ] S_END: $entry->[ S_END ]",
340 q_id => $entry->[ Q_ID ],
341 s_beg => $entry->[ S_BEG ],
342 s_end => $entry->[ S_END ],
343 strand => $entry->[ STRAND ],
347 y2 => $y1 + $cookie->{ 'FEAT_WIDTH' },
350 if ( $entry->[ STRAND ] eq '+' or $entry->[ STRAND ] eq '-' ) {
351 $feature->{ 'type' } = 'arrow';
353 $feature->{ 'type' } = 'rect';
356 push @features, $feature;
358 $y_max = Maasha::Calc::max( $y_max, $y_step * ( 1.1 + $cookie->{ 'FEAT_WIDTH' } ) );
360 push @features, feature_align( $entry, $beg, $y1, $factor, $cookie->{ 'FEAT_WIDTH' } ) if $entry->[ ALIGN ] ne '.';
362 $ladder[ $y_step ] = $x1 + $w;
366 $cookie->{ 'TRACK_OFFSET' } += $y_max + $cookie->{ 'TRACK_SPACE' };
368 return wantarray ? @features : \@features;
374 # Martin A. Hansen, November 2009.
376 # Add to feature track alignment info if the granularity is
378 # TODO: The printing of chars is imprecise.
380 my ( $entry, # Partial KISS entry
381 $beg, # base window beg
382 $y_offset, # y axis draw offset
383 $factor, # scale factor
384 $feat_height, # hight of feature in pixels
389 my ( $w, $align, $pos, $nt_before, $nt_after, $x1, @features );
391 $w = sprintf( "%.0f", 1 * $factor );
395 foreach $align ( split /,/, $entry->[ ALIGN ] )
397 if ( $align =~ /(\d+):([ATCGN-])>([ATCGN-])/ )
405 Maasha::Common::error( qq(BAD align descriptor: "$align") );
408 $x1 = sprintf( "%.0f", ( $entry->[ S_BEG ] + $pos - $beg ) * $factor );
412 line_width => $feat_height,
413 color => [ 1, 0, 0 ],
418 y2 => $y_offset + $feat_height,
421 if ( $w > $feat_height )
425 font_size => $feat_height + 2,
426 color => [ 0, 0, 0 ],
428 x1 => $x1 + sprintf( "%.0f", ( $w / 2 ) ) - $feat_height / 2,
429 y1 => $y_offset + $feat_height,
435 return wantarray ? @features : \@features;
439 sub track_feature_histogram
441 # Martin A. Hansen, November 2009.
443 # Create a feature track as a histogram using information
444 # from the index only thus avoiding to load features from the
447 my ( $cookie, # hashref with image draw metrics
448 $min, # minimum base position
449 $max, # maximum base position
450 $blocks, # list of blocks
455 my ( $hist_height, $bucket_width, $bucket_count, $min_bucket, $factor, $factor_heigth, $max_height, $block, $bucket_beg, $bucket_end, $i, @buckets, $h, $x, @hist );
457 return if $max <= $min;
459 $hist_height = 100; # pixels
461 $bucket_count = $cookie->{ 'IMG_WIDTH' } / $bucket_width;
462 $factor = ( $cookie->{ 'IMG_WIDTH' } / $bucket_width ) / ( $max - $min );
464 $min_bucket = 999999999;
467 foreach $block ( @{ $blocks } )
469 $bucket_beg = int( $block->{ 'BEG' } * $factor );
470 $bucket_end = int( $block->{ 'END' } * $factor );
472 $min_bucket = Maasha::Calc::min( $min_bucket, $bucket_beg );
474 for ( $i = $bucket_beg; $i < $bucket_end; $i++ )
476 $buckets[ $i ] += $block->{ 'COUNT' };
478 $max_height = Maasha::Calc::max( $max_height, $buckets[ $i ] );
482 if ( $max_height > 0 )
484 $factor_heigth = $hist_height / $max_height;
488 for ( $i = $min_bucket; $i < @buckets; $i++ )
490 if ( defined $buckets[ $i ] )
492 $h = sprintf( "%.0f", $buckets[ $i ] * $factor_heigth );
498 line_width => $bucket_width,
499 color => $cookie->{ 'FEAT_COLOR' },
500 title => "Features: $buckets[ $i ]",
502 y1 => $cookie->{ 'TRACK_OFFSET' } + $hist_height,
504 y2 => $cookie->{ 'TRACK_OFFSET' } + $hist_height - $h,
513 $cookie->{ 'TRACK_OFFSET' } += $hist_height + $cookie->{ 'TRACK_SPACE' };
515 return wantarray ? @hist : \@hist;
521 # Martin A. Hansen, November 2009.
523 # Returns the sequence from the contig in the beg/end interval
524 # contained in the cookie.
526 my ( $cookie, # cookie hash
531 my ( $path, $fh, $beg, $end, $len, $dna );
533 $path = path_seq( $cookie );
535 $beg = $cookie->{ 'S_BEG' };
536 $end = $cookie->{ 'S_END' };
539 $len = $end - $beg + 1;
542 $fh = Maasha::Filesys::file_read_open( $path );
544 $dna = Maasha::Filesys::file_read( $fh, $beg, $len );
546 $dna = Maasha::Seq::dna_revcomp( $dna ) if $cookie->{ 'STRAND' } eq '-';
548 Maasha::Seq::wrap( \$dna, 100 );
558 # Martin A. Hansen, November 2009.
560 # Returns the path to the sequence file for a specified
561 # contig as written in the cookie.
563 my ( $cookie, # cookie hash
570 die qq(ERROR: no USER in cookie.\n) if not $cookie->{ 'USER' };
571 die qq(ERROR: no CLADE in cookie.\n) if not $cookie->{ 'CLADE' };
572 die qq(ERROR: no GENOME in cookie.\n) if not $cookie->{ 'GENOME' };
573 die qq(ERROR: no ASSEMBLY in cookie.\n) if not $cookie->{ 'ASSEMBLY' };
574 die qq(ERROR: no CONTIG in cookie.\n) if not $cookie->{ 'CONTIG' };
577 $cookie->{ 'DATA_DIR' },
580 $cookie->{ 'CLADE' },
581 $cookie->{ 'GENOME' },
582 $cookie->{ 'ASSEMBLY' },
583 $cookie->{ 'CONTIG' },
588 die qq(ERROR: no such file: "$path".\n) if not -e $path;
596 # Martin A. Hansen, December 2009.
598 # Uses grep to search all tracks in all contigs
599 # for a given pattern and return a list of KISS entries.
601 my ( $cookie, # cookie hash
606 my ( $search_track, $search_term, $contig, @tracks, $track, $file, $line, $out_file, $fh, $entry, @entries, $track_name );
608 if ( $cookie->{ 'SEARCH' } =~ /^(.+)\s+track:\s*(.+)/i )
613 $search_track =~ tr/ /_/;
617 $search_term = $cookie->{ 'SEARCH' };
620 foreach $contig ( @{ $cookie->{ 'LIST_CONTIG' } } )
622 $cookie->{ 'CONTIG' } = $contig;
624 push @tracks, list_track_dir( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' } );
627 foreach $track ( @tracks )
631 $track_name = ( split "/", $track )[ -1 ];
633 next if $track_name !~ /$search_track/i;
636 $file = "$track/track_data.kiss";
640 $fh = Maasha::Filesys::file_read_open( $file );
642 while ( $line = <$fh> )
646 if ( $line =~ /$search_term/i )
648 $entry = Maasha::KISS::kiss_entry_parse( $line );
649 $entry = Maasha::KISS::kiss2biopiece( $entry );
650 push @entries, $entry;
658 return wantarray ? @entries : \@entries;
664 # Martin A. Hansen, December 2009.
666 # List all users directories in the ~/Data/Users
667 # directory with full path.
671 my ( @dirs, @users );
673 Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
675 @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users" );
677 @users = grep { $_ !~ /\/\.\.?$/ } @dirs;
679 return wantarray ? @users : \@users;
685 # Martin A. Hansen, December 2009.
687 # List all users in ~/Data/Users
691 my ( @dirs, $dir, @users );
693 @dirs = list_user_dir();
695 foreach $dir ( @dirs ) {
696 push @users, ( split "/", $dir )[ -1 ];
699 return wantarray ? @users : \@users;
705 # Martin A. Hansen, December 2009.
707 # List all clades for a given user in ~/Data/Users
709 my ( $user, # user for which to return clades
714 my ( @dirs, @clades );
716 Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
718 @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user" );
720 @clades = grep { $_ !~ /\/\.\.?$/ } @dirs;
722 return wantarray ? @clades : \@clades;
728 # Martin A. Hansen, December 2009.
730 # List all clades for a given user in ~/Data/Users
732 my ( $user, # user for which to return clades
737 my ( @dirs, $dir, @clades );
739 @dirs = list_clade_dir( $user );
741 foreach $dir ( @dirs ) {
742 push @clades, ( split "/", $dir )[ -1 ];
745 return wantarray ? @clades : \@clades;
751 # Martin A. Hansen, December 2009.
753 # List all genomes for a given user and clade in ~/Data/Users
755 my ( $user, # user for which to return genomes
756 $clade, # clade for which to return genomes
761 my ( @dirs, @genomes );
763 Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
765 @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade" );
767 @genomes = grep { $_ !~ /\/\.\.?$/ } @dirs;
769 return wantarray ? @genomes : \@genomes;
775 # Martin A. Hansen, December 2009.
777 # List all genomes for a given user and clade in ~/Data/Users
779 my ( $user, # user for which to return genomes
780 $clade, # clade for which to return genomes
785 my ( @dirs, $dir, @genomes );
787 @dirs = list_genome_dir( $user, $clade );
789 foreach $dir ( @dirs ) {
790 push @genomes, ( split "/", $dir )[ -1 ];
793 return wantarray ? @genomes : \@genomes;
797 sub list_assembly_dir
799 # Martin A. Hansen, December 2009.
801 # List all assemblies for a given user and clade and genome in ~/Data/Users
803 my ( $user, # user for which to return assemblies
804 $clade, # clade for which to return assemblies
805 $genome, # genome for which to return assemblies
810 my ( @dirs, @assemblies );
812 Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
814 if ( $user and $clade and $genome ) {
815 @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome" );
818 @assemblies = grep { $_ !~ /\/\.\.?$/ } @dirs;
820 return wantarray ? @assemblies : \@assemblies;
826 # Martin A. Hansen, December 2009.
828 # List all assemblies for a given user and clade and genome in ~/Data/Users
830 my ( $user, # user for which to return assemblies
831 $clade, # clade for which to return assemblies
832 $genome, # genome for which to return assemblies
837 my ( @dirs, $dir, @assemblies );
839 @dirs = list_assembly_dir( $user, $clade, $genome );
841 foreach $dir ( @dirs ) {
842 push @assemblies, ( split "/", $dir )[ -1 ];
845 return wantarray ? @assemblies : \@assemblies;
851 # Martin A. Hansen, December 2009.
853 # List all assemblies for a given user->clade->genome->assembly in ~/Data/Users
855 my ( $user, # user for which to return contigs
856 $clade, # clade for which to return contigs
857 $genome, # genome for which to return contigs
858 $assembly, # assembly for which to return contigs
863 my ( @dirs, @contigs );
865 Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
867 if ( $user and $clade and $genome and $assembly ) {
868 @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome/$assembly" );
871 @contigs = grep { $_ !~ /\/\.\.?$/ } @dirs;
873 return wantarray ? @contigs : \@contigs;
879 # Martin A. Hansen, December 2009.
881 # List all contigs for a given user->clade->genome->assembly in ~/Data/Users
883 my ( $user, # user for which to return contigs
884 $clade, # clade for which to return contigs
885 $genome, # genome for which to return contigs
886 $assembly, # assembly for which to return contigs
891 my ( @dirs, $dir, @contigs );
893 @dirs = list_contig_dir( $user, $clade, $genome, $assembly );
895 foreach $dir ( @dirs ) {
896 push @contigs, ( split "/", $dir )[ -1 ];
899 return wantarray ? @contigs : \@contigs;
905 # Martin A. Hansen, December 2009.
907 # List all tracks for a given user->clade->genome->assembly->contig in ~/Data/Users
909 my ( $user, # user for which to return tracks
910 $clade, # clade for which to return tracks
911 $genome, # genome for which to return tracks
912 $assembly, # assembly for which to return tracks
913 $contig, # contig for which to return tracks
918 my ( @dirs, @tracks );
920 Maasha::Common::error( 'BP_WWW not set in environment' ) if not $ENV{ 'BP_WWW' };
922 if ( -d "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome/$assembly/$contig/Tracks" ) {
923 @dirs = Maasha::Filesys::ls_dirs( "$ENV{ 'BP_WWW' }/Data/Users/$user/$clade/$genome/$assembly/$contig/Tracks" );
926 @tracks = grep { $_ !~ /\/\.\.?$/ } @dirs;
928 return wantarray ? @tracks : \@tracks;
934 # Martin A. Hansen, December 2009.
936 # List all tracks for a given user->clade->genome->assembly->contig in ~/Data/Users
938 my ( $user, # user for which to return tracks
939 $clade, # clade for which to return tracks
940 $genome, # genome for which to return tracks
941 $assembly, # assembly for which to return tracks
942 $contig, # contig for which to return tracks
947 my ( @dirs, $dir, @tracks );
949 @dirs = list_track_dir( $user, $clade, $genome, $assembly, $contig );
951 foreach $dir ( @dirs ) {
952 push @tracks, ( split "/", $dir )[ -1 ];
955 return wantarray ? @tracks : \@tracks;
961 # Martin A. Hansen, December 2009.
963 # Traverses all contigs for a given user->clade->genome->assembly and
964 # returns the maximum track's prefix value eg. 20 for 20_Genbank.
974 my ( @contigs, $contig, @tracks, $max );
976 @contigs = list_contigs( $user, $clade, $genome, $assembly );
978 foreach $contig ( @contigs ) {
979 push @tracks, list_tracks( $user, $clade, $genome, $assembly, $contig );
982 @tracks = sort @tracks;
984 if ( scalar @tracks > 0 and $tracks[ -1 ] =~ /^(\d+)/ ) {
994 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
1001 sub search_tracks_nc
1003 # Martin A. Hansen, December 2009.
1005 # Uses grep to search all tracks in all contigs
1006 # for a given pattern and return a list of KISS entries.
1008 my ( $cookie, # cookie hash
1013 my ( $search_track, $search_term, $contig, @tracks, $track, $file, @features, $track_name, $nc_list );
1015 if ( $cookie->{ 'SEARCH' } =~ /^(.+)\s+track:\s*(.+)/i )
1020 $search_track =~ tr/ /_/;
1024 $search_term = $cookie->{ 'SEARCH' };
1027 foreach $contig ( @{ $cookie->{ 'LIST_CONTIG' } } )
1029 $cookie->{ 'CONTIG' } = $contig;
1031 push @tracks, list_track_dir( $cookie->{ 'USER' }, $cookie->{ 'CLADE' }, $cookie->{ 'GENOME' }, $cookie->{ 'ASSEMBLY' }, $cookie->{ 'CONTIG' } );
1034 foreach $track ( @tracks )
1036 if ( $search_track )
1038 $track_name = ( split "/", $track )[ -1 ];
1040 next if $track_name !~ /$search_track/i;
1043 $file = "$track/track_data.kiss.json";
1047 $nc_list = Maasha::NClist::nc_list_retrieve( $file );
1048 push @features, Maasha::NClist::nc_list_search( $nc_list, $search_term, 12 );
1052 return wantarray ? @features : \@features;
1059 # Martin A. Hansen, November 2009.
1061 # Create a track with features. If there are more than $cookie->FEAT_MAX
1062 # features the track created will be a histogram, else linear.
1064 my ( $track, # path to kiss file with track data
1065 $cookie, # cookie hash
1070 my ( $index, $count, $track_name, $start, $end, $entries, $features );
1072 $start = $cookie->{ 'NAV_START' };
1073 $end = $cookie->{ 'NAV_END' };
1075 $index = Maasha::KISS::kiss_index_retrieve( "$track/track_data.kiss.index" );
1076 $count = Maasha::KISS::kiss_index_count( $index, $start, $end );
1078 $track_name = ( split "/", $track )[ -1 ];
1079 $track_name =~ s/^\d+_//;
1080 $track_name =~ s/_/ /g;
1085 font_size => $cookie->{ 'SEQ_FONT_SIZE' },
1086 color => $cookie->{ 'SEQ_COLOR' },
1088 y1 => $cookie->{ 'TRACK_OFFSET' },
1091 $cookie->{ 'TRACK_OFFSET' } += 10;
1093 if ( $count > $cookie->{ 'FEAT_MAX' } )
1095 $entries = Maasha::KISS::kiss_index_get_blocks( $index, $start, $end );
1096 push @{ $features }, track_feature_histogram( $cookie, $start, $end, $entries );
1100 $entries = Maasha::KISS::kiss_index_get_entries( "$track/track_data.kiss", $index, $start, $end );
1101 push @{ $features }, track_feature_linear( $cookie, $start, $end, $entries );
1104 return wantarray ? @{ $features } : $features;