$/ not reset by IOManager::read();

bradford_powell@med.unc.edu bradford_powell@med.unc.edu
Tue, 20 Jul 1999 15:11:32 -0400

Full_Name: Bradford Powell
Module: IOManager
Version: 1.5
OS: Debian GNU/Linux 2.0
Submission from: mslap0338.med.unc.edu (

I have been having problems with the parsing of
remotely-run blasts, in that the html files
were not properly parsed. So I tried some of the
demos. Oddly enough, run_blast_remote.pl worked,
but blast_seq.pl did not.

For a while, I thought this was a HTML.pm problem,
then I thought it was a seqtools.pl problem (since
blast_seq.pl did not work)... I think I have
stumbled upon the true cause. After the procedure
IOManager::read() is called by Fasta.pm, $/ has
been changed to "\n>", so when the html-stripping
code looks for the first line of the file, it
slurps the entire file.

--Bradford Powell

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