[Bioperl-l] errors when aligning

[Jason Stajich]

This is a bug in Root::IO wrt to running programs on windows -- I believe
you need to follow instructions at
http://bio.perl.org/bioperl-bugs.private/incoming?id=1224
and basically comment out these lines.

Ewan has fixed this on the main trunk.  This is meant to handle the weird
case of someone asking for clustalw exe like this '/clustalw'.
Alternatively I think the fix is to replace the offending line with
$exe =~ s/^\Q$PATHSEP//;
or
$exe =~ sm#^$PATHSEP##;
or
just comment out the line.  I can imagine weird cases where someone would
specify /clustalw IF they had tried and failed to construct the path
outside of the library and then passed the exe path to object thinking it
was properly constructed so I would like to see this check work.

We'll get this tracked down to the fullest before 1.2 - but since none of
the core developers run analyses on windows we'd appreciate feedback if
this fix works for you.

-jason
On Wed, 4 Sep 2002, Maurice Manning wrote:

> Hi Bioperl folks,
>
> I am just getting started with bioperl and trying some
> of the examples in the tutorial but I am having some
> difficulties.
>
> Trying to run a simple clustal example:
> use Bio::Seq;
> use Bio::AlignIO;
> use Bio::Tools::Run::Alignment::Clustalw;
>
> @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
> $factory =
> Bio::Tools::Run::Alignment::Clustalw->new(@params);
> #  Pass the factory a list of sequences to be aligned.
>
> $inputfilename = 'c:\\bioinfo\\data\\miniEcoli.fasta';
> $aln = $factory->align($inputfilename); # $aln is a
> SimpleAlign object.
>
> I get:
>    Error Trailing \ in regex m/^\/ at
> C:/Perl/site/lib/Bio/Root/IO.pm line 426.
>
> Am I configured incorrectly?  Is there some debug
> tips?
>
>
> Could I also get an example of how to get values out
> of a SeqStats and SeqWord objects for the simlpe cases
> of:
>  $seq_stats  =  Bio::Tools::SeqStats->new($seqobj);
>  $weight = $seq_stats->get_mol_wt();
>  $monomer_ref = $seq_stats->count_monomers();
>  $codon_ref = $seq_stats->count_codons();
>
>
> Any help would be great.  I am running under windows
> and have an ActiveState perl/bioperl install.
>
> Thanks,
> Mo
>
>
>
>
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-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu