[Bioperl-l] PrimarySeqI object Exception

sss lll nidage at yahoo.com
Thu Jul 6 18:13:12 UTC 2006


Hi there,

I encountered a problem while calling module
PrimarySeqI, with the following code:

my $db=Bio::DB::Fasta->new($fafile);
my $obj=$db->get_Seq_by_id($array_gene_name[$p]);
$seqio->write_seq($obj);

The error message was: 
MSG: Did not provide a valid Bio::PrimarySeqI object
STACK Bio::SeqIO::fasta::write_seq
/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/fasta.pm:178

We think it had to do with the lengh of the gene name.
For example the following gene name was a problem:

gi|59711891|ref|YP_204667.1| NAD-specific glutamate
dehydrogenase [Vibrio fischeri ES114]*VIB*COG2902*E

Any ideas on what happened?

Thanks

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