[Bioperl-l] Seqboot wrapper

Fields, Christopher J cjfields at illinois.edu
Tue Feb 4 18:26:47 UTC 2014


We can’t really help much w/o seeing your code and knowing what version of BioPerl you are using.  

My completely wild unsubstantiated and out of left-field guess is that you are passing in something other than an alignment *object*, for instance a file with the alignment in it.  Note that the code in question does create such an object using Bio::Tools::Run::Alignment::Clustalw; you can do this with a pre-made alignment using Bio::AlignIO.  This ($aln in the example) is then passed in to the wrapper.


On Feb 4, 2014, at 12:20 PM, ahlberg.gustav at gmail.com wrote:

> I have been trying to run seqboot via bioperl using the wrapper here
> http://doc.bioperl.org/bioperl-run/lib/Bio/Tools/Run/Phylo/Phylip/SeqBoot.html
> i keep getting the error message:
> MSG: Expecting a Bio::Align::AlignI object
> STACK Bio::Tools::Run::Phylo::Phylip::SeqBoot::_setinput 
> /opt/local/lib/perl5/site_perl/5.12.4/Bio/Tools/Run/Phylo/Phylip/Seqboot.pm:441
> STACK Bio::Tools::Run::Phylo::Phylip::SeqBoot::run 
> /opt/local/lib/perl5/site_perl/5.12.4/Bio/Tools/Run/Phylo/Phylip/Seqboot.pm:333
> STACK toplevel RIOpipe.pl:136
> But I cannot use Align::AlignI. It then tells me that:
> Use of new in Bio::Root::RootI is deprecated.  Please use Bio::Root::Root 
> instead
> I wanted to use Bioperl for seqboot so that my sequence names does not get 
> truncated.
> Best
> Gustav
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