[Bioperl-l] Bemusement with get_seq_by_gi in a CGI script

[Lincoln Stein]

Sorry about any confusion this caused.  However, it is mentioned in the docs 
for WebDBSeqI.  Perhaps the default should be changed to "tempfile", which 
should work in all cases.

Lincoln

On Wednesday 20 August 2003 01:05 pm, Jason Stajich wrote:
> > So your script is doing what it's supposed to, it's just that some other
> > stuff is getting out on STDOUT before your webserver is able to get in
> > on the act.
> >
> > Having played a bit, this proves to be interesting:
> >
> > #!/usr/bin/perl -w
> > use strict;
> > use Bio::DB::GenBank;
> >
> > close STDOUT;
> >
> > my $d = Bio::DB::GenBank->new();
> > my $seq = $d -> get_Seq_by_gi('163483');
> >
> >
> > This gives me:
> >
> > print() on closed filehandle STDOUT at
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/WebDBSeqI.pm line 701
> >
> > So WebDBSeqI.pm is usurping STDOUT as part of its query.  This probably
> > explains what you're getting.  Apache will redirect STDOUT straight to
> > the return stream for the connection.  This means it gets the output
> > intended for WbDBSeq and it appears in your programs output.  You then
> > get the output you printed.
>
> This is part of Lincoln's rechaining of the IO and using fork - looking
> at his comments in the code.
>     # Try to create a stream using POSIX fork-and-pipe facility.
>     # this is a *big* win when fetching thousands of sequences from
>     # a web database because we can return the first entry while
>     # transmission is still in progress.
>     # Also, no need to keep sequence in memory or in a temporary file.
>     # If this fails (Windows, MacOS 9), we fall back to non-pipelined
>     # access.
>
> You can turn this off by adding  to the DB::GenBank init
> my $db = new Bio::DB::GenBank(-retrievaltype => 'io_string');
>
> -retrievaltype => 'io_string' (for in-memory holding of the sequence
>                                 before parsing)
>  or
> -retrievaltype => 'temp'      (for use of tempfiles, but I'm not 100%
>                                 this code has gotten a workout to cleanup
>                                 until the program exits which might be
>                                 a problem for mod_perl running scripts)
>
> > If this is right, you should have some interesting error messages in
> > your logs if you run your script with warnings enabled.
> >
> > I can't see an immediate fix for this, short of running your fetch as a
> > completely detached process with a separate STDOUT, but that kind of
> > defeats the point of using mod-perl.  The use of a pipe from STDOUT to
> > read the results of a webquery seem pretty engrained into WebQueryI.pm
> > and it may not be trivial to change it.
> >
> > Maybe others will be able to think of a simpler work-round?
> >
> >
> > Simon.
> >
> > _______________________________________________
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> > Bioperl-l at portal.open-bio.org
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>
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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-- 
Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)