cleanup of BGB

git-svn-id: http://biopieces.googlecode.com/svn/trunk@830 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/intersect_records b/bp_bin/intersect_records
new file mode 100755 (executable)
index 0000000..81a390b
--- /dev/null
+++ b/bp_bin/intersect_records
@@ -0,0 +1,126 @@
+#!/usr/bin/env perl
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Intersect records in the stream based on overlapping intervals contained in values to specific keys.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+use warnings;
+use strict;
+use Maasha::Biopieces;
+use Data::Dumper;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $opt_key, $opt_strand, $found, $pos, $lookup_hash );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'key',     short => 'k', type => 'string', mandatory => 'yes', default => undef, allowed => undef, disallowed => undef },
+        { long => 'strand',  short => 's', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+        { long => 'inverse', short => 'i', type => 'flag',   mandatory => 'no',  default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$opt_key    = $options->{ 'key' };
+$opt_strand = $options->{ 'strand' };
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    if ( exists $record->{ 'S_ID' } and exists $record->{ 'S_BEG' } and exists $record->{ 'S_END' } )
+    {
+        $record->{ 'STRAND' } ||= '.';
+
+        if ( exists $record->{ $opt_key } )
+        {
+            map { $lookup_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->{ $_ } = 1 } ( $record->{ 'S_BEG' } .. $record->{ 'S_END' } );
+        }
+        else
+        {
+            $found = 0;
+
+            foreach $pos ( $record->{ 'S_BEG' } .. $record->{ 'S_END' } )
+            {
+                if ( $opt_strand )
+                {
+                    if ( exists $lookup_hash->{ $record->{ 'S_ID' } }->{ $record->{ 'STRAND' } }->{ $pos } )
+                    {
+                        $found = 1;
+
+                        last;
+                    }
+                }
+                else
+                {
+                    if ( exists $lookup_hash->{ $record->{ 'S_ID' } }->{ '+' }->{ $pos } or
+                         exists $lookup_hash->{ $record->{ 'S_ID' } }->{ '-' }->{ $pos }
+                    )
+                    {
+                        $found = 1;
+
+                        last;
+                    }
+                }
+            }
+
+            if ( (     $found and not $options->{ 'inverse' } ) or
+                 ( not $found and     $options->{ 'inverse' } )
+            )
+            {
+                Maasha::Biopieces::put_record( $record, $out );
+            }
+        }
+    }
+}
+
+# print Dumper( $lookup_hash );
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+__END__

diff --git a/code_perl/Maasha/BGB/Track.pm b/code_perl/Maasha/BGB/Track.pm
index ae60c8be2eb5a73e6e4f04b20c991edb739e7c01..64a3b6d3e5eff02455ff9ebc235455588a29900f 100644 (file)
--- a/code_perl/Maasha/BGB/Track.pm
+++ b/code_perl/Maasha/BGB/Track.pm
@@ -109,26 +109,30 @@ sub track_seq
 
     # Returns a list.
 
-    my ( $file, $fh, $seq, @chars, $factor, $i, @seq_list );
+    my ( $file, $fh, $seq, @chars, $factor, $x_offset, $i, @seq_list );
 
-    if ( $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' } + 1 <= 220 )
+    if ( $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' } + 1 <= 220 )  # only add sequence if less than or equal to 220.
     {
         $file = path_seq( $cookie );
         $fh   = Maasha::Filesys::file_read_open( $file );
-        $seq  = Maasha::Filesys::file_read( $fh, $cookie->{ 'NAV_START' } - 1, $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' } + 1 );
+        $seq  = Maasha::Filesys::file_read( $fh, $cookie->{ 'NAV_START' }, $cookie->{ 'NAV_END' } - $cookie->{ 'NAV_START' } + 1 );
         close $fh;
 
         @chars = split //, $seq;
 
         $factor = $cookie->{ 'IMG_WIDTH' } / @chars;
 
-        for ( $i = 0; $i < @chars; $i++ ) {
+        $x_offset = sprintf( "%.0f", ( $factor / 2 ) - ( $cookie->{ 'SEQ_FONT_SIZE' } / 2 ) );
+        $x_offset = 0 if $x_offset < 0;
+
+        for ( $i = 0; $i < @chars; $i++ )
+        {
             push @seq_list, {
                 type      => 'text',
                 txt       => $chars[ $i ],
                 font_size => $cookie->{ 'SEQ_FONT_SIZE' },
                 color     => $cookie->{ 'SEQ_COLOR' },
-                x1        => sprintf( "%.0f", $i * $factor ),
+                x1        => sprintf( "%.0f", $x_offset + $i * $factor ),
                 y1        => $cookie->{ 'TRACK_OFFSET' },
             };
         }

diff --git a/www/index.cgi b/www/index.cgi
index 99b535fdf8eb82c8decdf6574b991edc5b992921..cebfc1c6c184b4b3ca8525bf4a3da12e3b666f07 100755 (executable)
--- a/www/index.cgi
+++ b/www/index.cgi
@@ -579,7 +579,6 @@ sub page_browse
     push @html, section_taxonomy_table( $cookie );
     push @html, section_navigate( $cookie );
     push @html, section_browse( $cookie );
-    push @html, section_permalink( $cookie );
 
     return wantarray ? @html : \@html;
 }
@@ -882,37 +881,6 @@ sub section_browse
 }
 
 
-sub section_permalink
-{
-    # Martin A. Hansen, December 2009.
-
-    # Return HTML with a permanent link to current browser view.
-
-    my ( $cookie,   # cookie hash
-       ) = @_;
-
-    # Returns a list.
-
-    my ( $href, @html );
-
-    $href = join( "&",
-        "$cookie->{ 'SCRIPT' }?page=browse",
-        "user=$cookie->{ 'USER' }",
-        "clade=$cookie->{ 'CLADE' }",
-        "genome=$cookie->{ 'GENOME' }",
-        "assembly=$cookie->{ 'ASSEMBLY' }",
-        "contig=$cookie->{ 'CONTIG' }",
-        "nav_start=$cookie->{ 'NAV_START' }",
-        "nav_end=$cookie->{ 'NAV_END' }",
-        "session_id=$cookie->{ 'SESSION_ID' }",
-    );
-
-    push @html, Maasha::XHTML::p( txt => Maasha::XHTML::ln( txt => "Permalink", href => $href ), class => 'center' );
-
-    return wantarray ? @html : \@html;
-}
-
-
 sub section_export
 {
     # Martin A. Hansen, November 2009.