[Bioperl-l] SearchIO error

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed Jun 23 07:03:12 EDT 2004


I am using bioperl-1.4 now.  I seem to get an error when using SearchIO.
Perhaps I am not using it correctly?  My script is:

my $fh = new IO::File;
$fh->open("/usr/bin/blastall -p blastp -i test.fasta -d 10287/set2 |");

my $searchio = Bio::SearchIO->new(-format => 'blast', -fh => $fh);
my $result = $searchio->next_result;

my $search_out = Bio::SearchIO->new(-format => 'blast', -file =>


The error I get is:

-------------------- WARNING ---------------------
MSG: Writer not defined. Using a Bio::Search::Writer::HitTableWriter
Can't locate object method "new" via package
"Bio::Search::Writer::HitTableWriter" (perhaps you forgot to load
"Bio::Search::Writer::HitTableWriter"?) at
/usr/local/bioperl-1.4/Bio/SearchIO/blast.pm line 1493, <GEN0> line 397.

Can anyone be of help?


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