[Bioperl-l] swissprot giving no id exception
Guoneng Zhong
Guoneng.Zhong@med.nyu.edu
Fri, 12 Apr 2002 13:35:41 -0400
Hi,
I am wondering if others have this problem. Here's my code, followed by
the exception thrown. I get the same exception when I try to do a
next_seq on the sequenceIO object. The array of ids I send is verified
to contain non-empty ids. Now, I can't guarantee tht those ids are
valid, but if they are not, must an exception be thrown to ruin the
whole process? I tried to "catch" the exception using "eval" but
stranger things happen, like next_seq would give me the same sequence
again!
Thanks in advance!
G
my $sp = new Bio::DB::SwissProt;
my $sequenceIO = $sp->get_Stream_by_acc(\@ids);
my $fh = $sequenceIO->fh;
my $tmp = <$fh>;
-------------------- EXCEPTION --------------------
MSG: swissprot stream with no ID. Not swissprot in my book
STACK Bio::SeqIO::swiss::next_seq /Library/Perl/Bio/SeqIO/swiss.pm:155
STACK Bio::SeqIO::READLINE /Library/Perl/Bio/SeqIO.pm:570
STACK HypotheticalProteinSearch::retrieveSequences
HypotheticalProteinSearch.pm:37
STACK main::retrieveList retrieve_gpi.pl:54
STACK toplevel retrieve_gpi.pl:14
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