[Bioperl-l] can't start 'water'

[Jason Stajich]

do you have EMBOSS installed?
On Sat, 6 Sep 2003, Vesko Baev wrote:

> Hi,
> In my computer I have bioperl-pack & Bioperl-run-pack, and I HAVE water.pm,but:
> message in dos-prompt:
>
> -------------------- WARNING ---------------------
> MSG: Application [water] is not available!
> ---------------------------------------------------
> Can't call method "run" on an undefined value at water.pl line 22.
>
> Here is my script:
> #!usr/bin/perl
> use Bio::Factory::EMBOSS;
> use Bio::AlignIO;
>   my $seqobj1 = Bio::Seq->new(-seq => "gacgggtatctttaggcggacttagg");
>   my $seqobj2 = Bio::Seq->new(-seq => "gacgtgtatctttaggcggtcttacc");
>   my @seqs_to_check; # this would be a list of seqs to compare
>   push (@seqs_to_check,seqobj2);
>   # get an EMBOSS application object from the EMBOSS factory
>   $factory = new Bio::Factory::EMBOSS;
> #  $application = $factory->program('embossversion');
>   # run the application with an optional hash containing parameters
> #  $result = $application->run(); # returns a string or creates a file
> #  print $result . "\n";
>
>   $water = $factory->program('water');
>
>   # here is an example of running the application
>   # water can compare 1 seq against 1->many sequences
>   # in a database using Smith-Waterman
>
>   my $wateroutfile = 'mirna.water';
>   $water->run({ '-sequencea' => $seqobj1,
>
>               '-seqall'    => \@seqs_to_check,
>               '-gapopen'   => '10.0',
>               '-gapextend' => '0.5',
>               '-outfile'   => $wateroutfile});
>   # now you might want to get the alignment
>   use Bio::AlignIO;
>   my $alnin = new Bio::AlignIO(-format => 'emboss',
> 			       -file   => $wateroutfile);
>
>   while( my $aln = $alnin->next_aln ) {
>       # process the alignment -- these will be Bio::SimpleAlign objects
>   }
>
> AND when I wrote 'use Bio::Tools::Run::PiseApplication::water;'
> the message was:
> Can't locate XML/Parser/PerlSAX.pm in @INC?!?!?!
>
> WHAT TO DO?
> Vesko
> Thenks!!
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu