[Bioperl-l] Cannot download/find BPbl2seq module

[Brian Osborne]

Mark,

Bio::Tools::BPbl2seq was a part of the BLAST parsing BPLite package, written by Ian Korf way back when. BPLite was removed from Bioperl some years ago.

Brian O.


> On May 25, 2016, at 3:12 PM, Mark A Jensen <maj at fortinbras.us> wrote:
> 
> Oops, I am wrong about this. 
> There is no such module BPbl2seq in any distribution, there is a module Bio::AlignIO::bl2seq. My guess is this a module created by the author of the oaf tool that uses bioperl under the hood. You can get a missing module error sometimes if the module.is <http://module.is/> present but contains a syntax error.
> 
> On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <maj at fortinbras.us <mailto:maj at fortinbras.us>> wrote:
> 
> Jernej, this is a script that should appear in your path if you install bioperl from cpan and choose yes for the question "install scripts?"
> Mark
> 
> On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <turnsek at fas.harvard.edu <mailto:turnsek at fas.harvard.edu>> wrote:
> 
> 
> Dear BioPerl community,
> 
> 
> 
> 
> I am trying to use OAF <http://recode.ucc.ie/oaf/> - a Perl-based tool to analyze cDNA data - with a goal to detect antizyme or antizyme-like sequences. The publication describing the tool is available here <http://www.ncbi.nlm.nih.gov/pubmed/18384676>. I installed Perl (v5.22.2) and BioPerl (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (see this link <http://recode.ucc.ie/oaf/download>). What I tried to do next is replicate the "my_sequence" example listed on this website <http://recode.ucc.ie/oaf/download> using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary BioPerl module - BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore. I've talked to some Perl specialists around here and it seems like I should reinstall Perl and BioPerl versions that were present around the time this software was developed (2007/2008) with a rationale that they will carry all the necessary modules including BPbl2seq. 
> 
> 
> 
> I'd greatly appreciate if you could provide me with some tips on how to proceed. I am working on a Lenovo Yoga PC, 64-bit Windows 8.1.
> 
> 
> 
> 
> 
> I look forward to hearing from you.
> 
> Thank you and kind regards,
> 
> Jernej Turnsek
> 
> 
> 
> 
> 
> 
> 
> Jernej Turnsek 
> Ph.D. Candidate | Pamela Silver's Lab  <https://silver.med.harvard.edu/>
> Department of Systems Biology | Harvard Medical School
> 200 Longwood Ave | Boston, MA 02115
> (617) 797-5386 | Web <http://openwetware.org/wiki/User:JernejTurnsek> | LinkedIn <https://www.linkedin.com/in/jernejt> | @SynEnthu <https://twitter.com/>_______________________________________________
> Bioperl-l mailing list
> Bioperl-l at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/bioperl-l

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/bioperl-l/attachments/20160525/acd79824/attachment.html>