cleanup BGB stuff

git-svn-id: http://biopieces.googlecode.com/svn/trunk@845 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/BGB_intersect b/bp_bin/BGB_intersect
index 7561872d49fb2f28315d79866064715765333213..b6a5bfedc931cc558fc6fc89d75ba4418d9adfde 100755 (executable)
--- a/bp_bin/BGB_intersect
+++ b/bp_bin/BGB_intersect
@@ -21,7 +21,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# List all tracks availible in a local installation of the Biopieces Genome Browser.
+# Intersects two tracks in the Biopieces Genome Browser.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 

diff --git a/bp_bin/BGB_upload b/bp_bin/BGB_upload
index 611f60425bc5122326ca8876944fcf94960bd68d..a88576cb50885be478a7e14816b7c0b660ab60ca 100755 (executable)
--- a/bp_bin/BGB_upload
+++ b/bp_bin/BGB_upload
@@ -21,7 +21,7 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# Write Biopiece records to the KISS Genome browser.
+# Write Biopiece records to the Biopieces Genome browser.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 

diff --git a/bp_bin/assemble_contigs b/bp_bin/assemble_contigs
index 3e73a763b82cf101873fcc83b5b09d4f75517cba..8976cc8e09a9b928a3d71ac425a556f51c81bf38 100755 (executable)
--- a/bp_bin/assemble_contigs
+++ b/bp_bin/assemble_contigs
@@ -106,9 +106,9 @@ foreach $s_id ( keys %{ $contig_hash } )
 
             $new_record->{ 'S_ID' }        = $s_id;
             $new_record->{ 'STRAND' }      = $strand;
+            $new_record->{ 'S_BEG' }       = $beg;
+            $new_record->{ 'S_END' }       = $end;
             $new_record->{ 'CONTIG_ID' }   = $contig;
-            $new_record->{ 'CONTIG_BEG' }  = $beg;
-            $new_record->{ 'CONTIG_END' }  = $end;
             $new_record->{ 'CONTIG_LEN' }  = $end - $beg + 1;
             $new_record->{ 'CONTIG_MIN' }  = $min;
             $new_record->{ 'CONTIG_MAX' }  = $max;

diff --git a/bp_bin/create_blast_index b/bp_bin/create_blast_index
index 6cbd2bf62d5a031eda9454382419e479ae666b5f..9c04c04ff7ec416c4f42207dd2e44b023f98bbf6 100755 (executable)
--- a/bp_bin/create_blast_index
+++ b/bp_bin/create_blast_index
@@ -88,7 +88,7 @@ else
     Maasha::Common::run( "formatdb", "$arg -l /dev/null" );
 }
 
-Maasha::Filesys::dir_create( $options->{ 'directory' } );
+Maasha::Filesys::dir_create_if_not_exists( $options->{ 'directory' } );
 
 unlink $file_tmp;
 

diff --git a/code_perl/Maasha/KISS.pm b/code_perl/Maasha/KISS.pm
index 85a8105d1d2c3e00fc5cbb5b51476b03bf648154..539e501412104e531a86ceac316d2ba73021d965 100644 (file)
--- a/code_perl/Maasha/KISS.pm
+++ b/code_perl/Maasha/KISS.pm
@@ -592,6 +592,13 @@ sub biopiece2kiss
 
     # Returns a hashref
 
+    if ( not defined $record->{ 'S_ID' }  and
+         not defined $record->{ 'S_BEG' } and
+         not defined $record->{ 'S_END' } )
+    {
+        return undef;
+    }
+
     $record->{ 'SCORE' }       ||= $record->{ 'E_VAL' } || ".";
     $record->{ 'HITS' }        ||= ".";
     $record->{ 'BLOCK_COUNT' } ||= ".";