Bio::Tools::Blast->new fails

ers007@email.mot.com ers007@email.mot.com
Wed, 18 Aug 1999 18:20:43 -0400


Full_Name: Rob Svirskas
Module: Blast.pm
Version: Blast.pm,v 1.8.2.3 1999/06/25 12:15:48
OS: SunOS 5.6
Submission from: netcache1.mot.com (129.188.33.221)


I am running a probram via the web (CGI.pm) that
performs a BLAST job and uses
Bio::Tools::Blast->new. I get the following error:

-------------------- EXCEPTION --------------------
MSG: Can't determine program type from BLAST report.
NOTE: Checked for: blastp blastn blastx tblastn tblastx.
CONTEXT: Error in object Bio::Tools::Blast "anonymous Bio::Tools::Blast"
SCRIPT: /usr/local/bin/make_probes
STACK: 
Bio::Tools::Blast::_parse_header(1899)
Bio::Tools::Blast::__ANON__(1744)
Bio::Root::IOManager::read(736)
Bio::Root::Object::read(2055)
Bio::Tools::Blast::_parse_blast_stream(1623)
Bio::Tools::Blast::parse(1474)
Bio::Tools::SeqAnal::_initialize(286)
Bio::Root::Object::new(455)
main::BLASTProbes(828)
main::/usr/local/bin/make_probes(1644)
---------------------------------------------------

The line it fails on is:
if($data =~ /(<\w+>)?(T?BLAST[NPX])\s+(.+?)$Newline/so)

The regexp returns FALSE since $Newline is undefined.
The web server is running as "nobody", and I
believe that "nobody" has no "newline" defined. My
fix for it was to explicitly define $Newline.


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