[Bioperl-l] recovering blast query_name
Lewis Lukens
llukens@uoguelph.ca
Wed, 20 Nov 2002 15:49:17 -0500
Hello,
Sorry for a basic question... I have been trying to use the
Bio::Tools:Run:RemoteBlast module to blast a single file with many
fasta formated sequences against ncbi nt and parse the blast reports.
Almost everything is working well. I get all the hit and hsp
features for all the hits. I can recover the query sequence, but I
can't seem to recover the query sequence names. How does one do this?
I used almost the exact code as in the Remoteblast Synopsis
http://doc.bioperl.org/releases/bioperl-1.0.2/Bio/Tools/Run/RemoteBlast.html
in this code, this expression works:
print "db is ", $result->database_name(), "\n";
but, these expressions return empty fields:
my $name = $result->query_name();
my $desc = $result->query_description();
my $acc= $result->query_accession();
I have been using SearchIO to parse blast output files and never had
this problem before. Any ideas?
Thanks much,
Lewis
--
Lewis Lukens
Assistant Professor
Department of Plant Agriculture
Univ. of Guelph, Guelph, Ontario. N1G 2W1
Tel: (519) 824- 4120 ext 2304