[Bioperl-guts-l] [15137] bioperl-live/trunk/Bio/DB/SeqFeature: added simple feature deletion script

Lincoln Stein lstein at dev.open-bio.org
Wed Dec 10 13:26:31 EST 2008


Revision: 15137
Author:   lstein
Date:     2008-12-10 13:26:31 -0500 (Wed, 10 Dec 2008)

Log Message:
-----------
added simple feature deletion script

Modified Paths:
--------------
    bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/mysql.pm
    bioperl-live/trunk/Bio/DB/SeqFeature/Store.pm

Modified: bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/mysql.pm
===================================================================
--- bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/mysql.pm	2008-12-10 16:52:17 UTC (rev 15136)
+++ bioperl-live/trunk/Bio/DB/SeqFeature/Store/DBI/mysql.pm	2008-12-10 18:26:31 UTC (rev 15137)
@@ -1181,7 +1181,7 @@
     $sth2->execute($cid);
     my ($count) = $sth2->fetchrow_array;
     if ($count == 1) {
-        $self->_deleteid($cid) || $self->throw("Couldn't remove subfeature!");
+        $self->_deleteid($cid) || warn "An error occurred while removing subfeature id=$cid. Perhaps it was previously deleted?\n";
     }
   }
   for my $table ($self->all_tables) {

Modified: bioperl-live/trunk/Bio/DB/SeqFeature/Store.pm
===================================================================
--- bioperl-live/trunk/Bio/DB/SeqFeature/Store.pm	2008-12-10 16:52:17 UTC (rev 15136)
+++ bioperl-live/trunk/Bio/DB/SeqFeature/Store.pm	2008-12-10 18:26:31 UTC (rev 15137)
@@ -43,7 +43,7 @@
   @features = $db->get_features_by_alias('sma-3');
 
   # ...by type
-  @features = $db->get_features_by_name('gene');
+  @features = $db->get_features_by_type('gene');
 
   # ...by location
   @features = $db->get_features_by_location(-seq_id=>'Chr1',-start=>4000,-end=>600000);




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