[Biophp-dev] AFter Sean's brain stops hurting

[Serge Gregorio]

Sean,

I'm writing some PHP-Perl interface code and I can't seem
to make this Perl script (ps_scan.pl) run on a web server
(other than my own local copy).  See attached file (or if
it's not here, it's probably in your private email box).

It's a binary for a Linux/Intel box.  Binaries for other 
platforms are at the PROSITE site: 

   ftp://us.expasy.org/databases/prosite/tools/ps_scan/

Would it be possible for you to upload it to some HTDOCS
(web document root) folder at bioinformatics.org?  Plus
these two files:

php_perl.php

   <?php
      print "<H2>Test PHP script that runs a Perl scrip</H2>";
      $output = `perl ps_scan.pl seq.dat`
      print $output;
  ?>

probe.dat

   >gi|24653663|ref|NM_079018.2| Unknown  CG10119-PA (LamC), prot
   MFNFVLLAILCKIVCLGLKLILLTLRHPSINLSVSNLVKHFQF 

Or, if it's too much of a bother to you, could you give me 
write access to the biophp project's HTDOCS folder?  Thanks!

Also, I've finally thought of an immediate use for your eFetch/
eUtils set of modules.  I'd like to submit a protein sequence
(like the one shown above) to NCBI'S BLAST server and get some
matches, from within a PHP script.  Could you provide some info
on how your code can be used for this purpose (or how it can be
extended/modified to do this)?  Or better yet, maybe you could
do the necessary coding (when your BRAIN STOPS HURTING, that is).

I've finally read your code (parse, parse_fasta, seqfactory, etc), and will be giving more specific comments/questions soon.

Thanks!  

Regards,

Serge


Need a new email address that people can remember
Check out the new EudoraMail at
http://www.eudoramail.com