[Bioperl-l] Seqboot wrapper

Fields, Christopher J cjfields at illinois.edu
Tue Feb 4 19:25:42 UTC 2014

(pls keep replies on list)

Welcome to bioinformatics, I guess?


On Feb 4, 2014, at 1:04 PM, Gustav Ahlberg <ahlberg.gustav at gmail.com<mailto:ahlberg.gustav at gmail.com>> wrote:

Thank you for your help anyway. Doesn't matter because in order to not truncate the names I need to make the alignment with
Simple align. And since I need to use mafft with certain options I cannot use that. So then I then there is no need to use seqboot via bioperl I guess. And if I am not able to keep the protein names in a special format I can't use them for an other program. And the list goes on and on and format formats formats and catch 22...

2014-02-04 Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>>:

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<mailto: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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