[Bioperl-l] Codeml.pm/PAML.pm

[Derek Gatherer]

Hi

I'm running the script in scripts/utilities/pairwise_kaks.PLS , but it 
chokes when it gets to the line:

my $result = $parser->next_result;

the output is:

____________________

  CLUSTAL W (1.83) Multiple Sequence Alignments



Sequence format is Pearson
Sequence 1: MERLIN_UL150.CDS.EXP      639 aa
Sequence 2: TOLEDO_UL150.CDS.EXP      639 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score:  94
Guide tree        file created:   [/tmp/9TloZHefb1/Xk3b0BFDEn.dnd]
Start of Multiple Alignment
There are 1 groups
Aligning...
Group 1: Sequences:   2      Score:13481
Alignment Score 3765
GCG-Alignment file created      [/tmp/9TloZHefb1/aGgun5VY9E]
Use of uninitialized value in pattern match (m//) at 
/usr/lib/perl-5.8.0/lib/site_perl/5.8.0/Bio/Tools/Phylo/PAML.pm line 524, 
<GEN2> line 89.

_______________________

so I seem to be getting as far as actually making the parser with 
$kaks_factory->run(), but then that parser won't run next_result().  The 
line in PAML.pm that causes the problem is:

while( $rest =~
                /(\-?\d+(\.\d+)?)\s*\(\-?(\d+(\.\d+)?)\s+(\-?\d+(\.\d+)?)\)/g )

Is this a PAML configuration problem? or is it my input format (it looks 
like okay FASTA to me)

Cheers
Derek