fixed a number of issues - grave bug in complement_seq!

git-svn-id: http://biopieces.googlecode.com/svn/trunk@850 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/BGB_upload b/bp_bin/BGB_upload
index a88576cb50885be478a7e14816b7c0b660ab60ca..ba8b9d05685612bbd9a7d2174f4d1ae29f14a24f 100755 (executable)
--- a/bp_bin/BGB_upload
+++ b/bp_bin/BGB_upload
@@ -121,7 +121,7 @@ else
 
     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 ) ) 

diff --git a/bp_bin/complement_seq b/bp_bin/complement_seq
index 348e0580640c1e2a97c18cbd156d543bd08e67cc..10a3a043d5e607b921d409d07d6cbae010a8a4fb 100755 (executable)
--- a/bp_bin/complement_seq
+++ b/bp_bin/complement_seq
@@ -50,9 +50,9 @@ while ( $record = Maasha::Biopieces::get_record( $in ) )
             $type = Maasha::Seq::seq_guess_type( $record->{ "SEQ" } );
         }
         
-        if ( $type eq "rna" ) {
+        if ( $type eq "RNA" ) {
             Maasha::Seq::rna_comp( \$record->{ "SEQ" } );
-        } elsif ( $type eq "dna" ) {
+        } elsif ( $type eq "DNA" ) {
             Maasha::Seq::dna_comp( \$record->{ "SEQ" } );
         }
     }

diff --git a/code_perl/Maasha/BGB/Draw.pm b/code_perl/Maasha/BGB/Draw.pm
index 7053aa4fad3503a334dec80ead00a7a95e3c3169..907b8173e7e65258e8f59389eed6fbdc61703e77 100644 (file)
--- a/code_perl/Maasha/BGB/Draw.pm
+++ b/code_perl/Maasha/BGB/Draw.pm
@@ -120,6 +120,20 @@ sub palette
         [ 130,  70,  70 ],
         [  70, 170, 130 ],
         [ 130, 170,  50 ],
+        [  30, 130, 130 ],
+        [  30,  50, 150 ],
+        [ 130, 130,  50 ],
+        [ 130,  90, 130 ],
+        [ 130,  70,  70 ],
+        [  70, 170, 130 ],
+        [ 130, 170,  50 ],
+        [  30, 130, 130 ],
+        [  30,  50, 150 ],
+        [ 130, 130,  50 ],
+        [ 130,  90, 130 ],
+        [ 130,  70,  70 ],
+        [  70, 170, 130 ],
+        [ 130, 170,  50 ],
     ];  
     
     $color = $palette->[ $i ];