[Bioperl-l] Cannot download/find BPbl2seq module

Wed May 25 19:12:52 UTC 2016

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 present but contains a syntax error.

On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen < maj at fortinbras.us 
[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 
[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/]
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