[Bioperl-l] Bio::Root::Exception when using Bio::Seq

Clarke, Wayne ClarkeW at AGR.GC.CA
Mon Jun 19 18:34:37 EDT 2006


Hi,

I am getting the following warning and then exception 

 

-------------------- WARNING ---------------------

MSG: seq doesn't validate, mismatch is 1

---------------------------------------------------

 

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: Attempting to set the sequence to [ACTG*] which does not look
healthy

 

NOTE: ACTG* represents a sequence of those 4 characters(a valid DNA
sequence)

 

when extracting display name and sequence from a MYSQL database. My code
is as follows:

 

my $sql = "select Clone_Name,Sequence from tbl_bgene";

     my $sth = $dbh->prepare($sql);

     $sth->execute();

     while (my $hash = $sth->fetchrow_hashref()) {

          # print("Name: ".$hash->{'Clone_Name'}."\n");

          my $seq = new Bio::Seq(  -display_id     =>
$hash->{'Clone_Name'},

                                   -seq      =>   $hash->{'Sequence'});

          $handle->write_seq($seq);

          # print("Sequence: ".$hash->{'Sequence'}."\n");

     }

 

For some reason it is failing on a particular sequence, which is a valid
DNA sequence. If anyone has any ideas on why this is I would appreciate
it.

 

Thanks, Wayne




More information about the Bioperl-l mailing list