$start = $cookie->{ 'NAV_START' };
$end = $cookie->{ 'NAV_END' };
- $index = Maasha::KISS::kiss_index_retrieve( "$track/track_data.kiss.json" );
+ $index = Maasha::KISS::kiss_index_retrieve( "$track/track_data.kiss.index" );
$count = Maasha::KISS::kiss_index_count( $index, $start, $end );
$track_name = ( split "/", $track )[ -1 ];
if ( $count > $cookie->{ 'FEAT_MAX' } )
{
-# $entries = Maasha::KISS::kiss_index_get_blocks( $index, $start, $end );
-# push @{ $features }, track_feature_histogram( $cookie, $start, $end, $entries );
+ $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( $index, $start, $end );
+ $entries = Maasha::KISS::kiss_index_get_entries( "$track/track_data.kiss", $index, $start, $end );
push @{ $features }, track_feature_linear( $cookie, $start, $end, $entries );
}
if ( $w >= 1 )
{
- foreach $align ( split /,/, $entry->{ 'ALIGN' } )
+ foreach $align ( split /,/, $entry->[ ALIGN ] )
{
if ( $align =~ /(\d+):([ATCGN-])>([ATCGN-])/ )
{
# Returns a list.
- my ( $search_track, $search_term, $contig, @tracks, $track, $file, @features, $track_name, $nc_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 )
{
next if $track_name !~ /$search_track/i;
}
- $file = "$track/track_data.kiss.json";
+ $file = "$track/track_data.kiss";
if ( -f $file )
{
- $nc_list = Maasha::NClist::nc_list_retrieve( $file );
- push @features, Maasha::NClist::nc_list_search( $nc_list, $search_term, 12 );
+ $fh = Maasha::Filesys::file_read_open( $file );
+
+ while ( $line = <$fh> )
+ {
+ chomp $line;
+
+ if ( $line =~ /$search_term/i )
+ {
+ $entry = Maasha::KISS::kiss_entry_parse( $line );
+ push @entries, $entry;
+ }
+ }
+
+ close $fh;
}
}
- return wantarray ? @features : \@features;
+ return wantarray ? @entries : \@entries;
}
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 )
+ {
+ $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.json";
+
+ if ( -f $file )
+ {
+ $nc_list = Maasha::NClist::nc_list_retrieve( $file );
+ push @features, Maasha::NClist::nc_list_search( $nc_list, $search_term, 12 );
+ }
+ }
+
+ return wantarray ? @features : \@features;
+}
use warnings;
use strict;
use Data::Dumper;
+use JSON::XS;
use Maasha::Common;
use Maasha::Filesys;
-use Maasha::NClist;
use Maasha::Align;
use vars qw( @ISA @EXPORT );
{
# Martin A. Hansen, December 2009.
- # TODO find out what uses this and kill it!
-
# Parses a line with a KISS entry.
my ( $line, # KISS line to parse
Maasha::Common::error( qq(BAD kiss entry: $line) ) if not @fields == 12;
- $entry{ 'S_ID' } = $fields[ S_ID ];
- $entry{ 'S_BEG' } = $fields[ S_BEG ];
- $entry{ 'S_END' } = $fields[ S_END ];
- $entry{ 'Q_ID' } = $fields[ Q_ID ];
- $entry{ 'SCORE' } = $fields[ SCORE ];
- $entry{ 'STRAND' } = $fields[ STRAND ];
- $entry{ 'HITS' } = $fields[ HITS ];
- $entry{ 'ALIGN' } = $fields[ ALIGN ];
- $entry{ 'BLOCK_COUNT' } = $fields[ BLOCK_COUNT ];
- $entry{ 'BLOCK_BEGS' } = $fields[ BLOCK_BEGS ];
- $entry{ 'BLOCK_LENS' } = $fields[ BLOCK_LENS ];
- $entry{ 'BLOCK_TYPE' } = $fields[ BLOCK_TYPE ];
-
- return wantarray ? %entry : \%entry;
+ return wantarray ? @fields : \@fields;
}
}
-sub kiss_index_old
+sub kiss_index
{
# Martin A. Hansen, December 2009.
# Creates a lookup index of a sorted KISS file.
- my ( $file, # path to KISS file
+ my ( $file, # path to KISS file
) = @_;
# Returns nothing.
}
-sub kiss_index
+sub kiss_index_offset
{
- # Martin A. Hansen, February 2010.
+ # Martin A. Hansen, December 2009.
- # Creates a NC list index of a sorted KISS file.
+ # Given a KISS index and a begin position,
+ # locate the offset closest to the begin position,
+ # and return this.
- my ( $file, # path to KISS file
+ my ( $index, # KISS index
+ $beg, # begin position
) = @_;
- # Returns nothing.
-
- my ( $fh, $line, @fields, $nc_list );
+ # Returns a number.
- $fh = Maasha::Filesys::file_read_open( $file );
+ my ( $bucket );
- while ( $line = <$fh> )
- {
- chomp $line;
+ Maasha::Common::error( qq(Negative begin position: "$beg") ) if $beg < 0;
- @fields = split "\t", $line;
+ $bucket = int( $beg / BUCKET_SIZE );
- if ( not defined $nc_list ) {
- $nc_list = [ [ @fields ] ];
- } else {
- Maasha::NClist::nc_list_add( $nc_list, [ @fields ], INDEX_END, INDEX );
- }
- }
+ $bucket = scalar @{ $index } if $bucket > scalar @{ $index };
- close $fh;
+ while ( $bucket >= 0 )
+ {
+ return $index->[ $bucket ]->[ OFFSET ] if defined $index->[ $bucket ];
- Maasha::NClist::nc_list_store( $nc_list, "$file.json" );
+ $bucket--;
+ }
}
-sub kiss_index_offset
+sub kiss_index_count
{
# Martin A. Hansen, December 2009.
- # Given a KISS index and a begin position,
- # locate the offset closest to the begin position,
+ # Given a KISS index and a begin/end interval
+ # sum the number of counts in that interval,
# and return this.
- my ( $index, # KISS index
- $beg, # begin position
+ my ( $index, # KISS index
+ $beg, # Begin position
+ $end, # End position
) = @_;
# Returns a number.
- my ( $bucket );
+ my ( $bucket_beg, $bucket_end, $count, $i );
Maasha::Common::error( qq(Negative begin position: "$beg") ) if $beg < 0;
- $bucket = int( $beg / BUCKET_SIZE );
+ $bucket_beg = int( $beg / BUCKET_SIZE );
+ $bucket_end = int( $end / BUCKET_SIZE );
- $bucket = scalar @{ $index } if $bucket > scalar @{ $index };
+ $bucket_end = scalar @{ $index } if $bucket_end > scalar @{ $index };
- while ( $bucket >= 0 )
- {
- return $index->[ $bucket ]->[ OFFSET ] if defined $index->[ $bucket ];
+ $count = 0;
- $bucket--;
+ for ( $i = $bucket_beg; $i <= $bucket_end; $i++ ) {
+ $count += $index->[ $i ]->[ COUNT ] if defined $index->[ $i ];
}
+
+ return $count;
}
-sub kiss_index_count
+sub kiss_index_count_nc
{
# Martin A. Hansen, December 2009.
# along with a beg/end interval, locate all entries
# in that interval and return those.
- my ( $index, # KISS index
+ my ( $file, # path to KISS file
+ $index, # KISS index
$beg, # interval begin
$end, # interval end
) = @_;
# Returns a list.
- my ( $features );
+ my ( $offset, $fh, $entry, @entries );
- $features = Maasha::NClist::nc_list_get_interval( $index, $beg, $end, INDEX_BEG, INDEX_END, INDEX );
+ # $offset = kiss_index_offset( $index, $beg );
- return wantarray ? @{ $features } : $features;
+ $fh = Maasha::Filesys::file_read_open( $file );
+
+ # sysseek( $fh, $offset, 0 );
+
+ while ( $entry = Maasha::KISS::kiss_entry_get( $fh ) )
+ {
+ push @entries, $entry if $entry->[ S_END ] > $beg;
+
+ last if $entry->[ S_BEG ] > $end;
+ }
+
+ close $fh;
+
+ return wantarray ? @entries : \@entries;
+}
+
+
+sub kiss_index_get_entries_OLD
+{
+ # Martin A. Hansen, November 2009.
+
+ # Given a path to a KISS file and a KISS index
+ # along with a beg/end interval, locate all entries
+ # in that interval and return those.
+
+ my ( $file, # path to KISS file
+ $index, # KISS index
+ $beg, # interval begin
+ $end, # interval end
+ ) = @_;
+
+ # Returns a list.
+
+ my ( $offset, $fh, $entry, @entries );
+
+ $offset = kiss_index_offset( $index, $beg );
+
+ $fh = Maasha::Filesys::file_read_open( $file );
+
+ sysseek( $fh, $offset, 0 );
+
+ while ( $entry = Maasha::KISS::kiss_entry_get( $fh ) )
+ {
+ push @entries, $entry if $entry->[ S_END ] > $beg;
+
+ last if $entry->[ S_BEG ] > $end;
+ }
+
+ close $fh;
+
+ return wantarray ? @entries : \@entries;
}
# Returns nothing.
- Maasha::Filesys::file_store( $path, $index );
+ my ( $fh, $json );
+
+ $json = JSON::XS::encode_json( $index );
+
+ $fh = Maasha::Filesys::file_write_open( $path );
+
+ print $fh $json;
+
+ close $fh;
}
# Returns a data structure.
- my ( $index );
+ my ( $fh, $json, $index );
- $index = Maasha::NClist::nc_list_retrieve( $path );
+ local $/ = undef;
+
+ $fh = Maasha::Filesys::file_read_open( $path );
+
+ $json = <$fh>;
+
+ close $fh;
+
+ $index = JSON::XS::decode_json( $json );
return wantarray ? @{ $index } : $index;
}
1;
+__END__
+
+sub kiss_index_nc
+{
+ # Martin A. Hansen, February 2010.
+
+ # Creates a NC list index of a sorted KISS file.
+
+ my ( $file, # path to KISS file
+ ) = @_;
+
+ # Returns nothing.
+
+ my ( $fh, $line, @fields, $nc_list );
+
+ $fh = Maasha::Filesys::file_read_open( $file );
+
+ while ( $line = <$fh> )
+ {
+ chomp $line;
+
+ @fields = split "\t", $line;
+
+ if ( not defined $nc_list ) {
+ $nc_list = [ [ @fields ] ];
+ } else {
+ Maasha::NClist::nc_list_add( $nc_list, [ @fields ], INDEX_END, INDEX );
+ }
+ }
+
+ close $fh;
+
+ Maasha::NClist::nc_list_store( $nc_list, "$file.json" );
+}
+
+
+sub kiss_index_get_entries_nc
+{
+ # Martin A. Hansen, November 2009.
+
+ # Given a path to a KISS file and a KISS index
+ # along with a beg/end interval, locate all entries
+ # in that interval and return those.
+
+ my ( $index, # KISS index
+ $beg, # interval begin
+ $end, # interval end
+ ) = @_;
+
+ # Returns a list.
+
+ my ( $features );
+
+ $features = Maasha::NClist::nc_list_get_interval( $index, $beg, $end, INDEX_BEG, INDEX_END, INDEX );
+
+ return wantarray ? @{ $features } : $features;
+}
+
+
+sub kiss_index_retrieve_nc
+{
+ # Martin A. Hansen, November 2009.
+
+ # Retrieves a KISS index from a file.
+
+ my ( $path, # Path to KISS index
+ ) = @_;
+
+ # Returns a data structure.
+
+ my ( $index );
+
+ $index = Maasha::NClist::nc_list_retrieve( $path );
+
+ return wantarray ? @{ $index } : $index;
+}
projects / biopieces.git / commitdiff