Cannot download/find Bio::Tools::BPbl2seq module

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Cannot download/find Bio::Tools::BPbl2seq module

Turnsek, Jernej

Dear BioPerl community,


I am trying to use 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. 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). What I tried to do next is replicate the "my_sequence" example listed on this website using the attached oaf.pl script and .fasta file, but ended up stuck with the message you can also find attached. It looks like I am missing a necessary BioPerl module - Bio::Tools: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'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.


Thank you and kind regards,


Jernej Turnsek




Jernej Turnsek 
Ph.D. Candidate | Pamela Silver's Lab 
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
(617) 797-5386 | Web | LinkedIn | @SynEnthu


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oaf.pl (12K) Download Attachment
mysequence.fasta (1K) Download Attachment
JT_oaf.pl_test .png (3M) Download Attachment
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Re: Cannot download/find Bio::Tools::BPbl2seq module

James E Keenan
On 05/17/2016 12:19 PM, Turnsek, Jernej 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 oaf.pl script and .fasta file, but ended up stuck with the message you can also find attached. It looks like I am missing a necessary BioPerl module - Bio::Tools:BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore.
>
>

This message only showed up in my Inbox today -- nearly 6 months after
it was sent!

The module you were looking for is cited in the DEPRECATED file in the
git repo bioperl-live.

Bio::Tools::BPbl2seq          1.5      1.6    use Bio::SearchIO

So I suppose you should try Bio::SearchIO if you are still working on
this problem.


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Re: Cannot download/find Bio::Tools::BPbl2seq module

Fields, Christopher J

On 11/10/16, 2:16 PM, "Bioperl-l on behalf of James E Keenan" <bioperl-l-bounces+cjfields=[hidden email] on behalf of [hidden email]> wrote:

>On 05/17/2016 12:19 PM, Turnsek, Jernej 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 oaf.pl script and .fasta file, but ended up stuck with the message you can also find attached. It looks like I am missing a necessary BioPerl module - Bio::Tools:BPbl2seq - which I couldn't download from CPAN. I tried to locate it manually online, but it looks like it doesn't exist anymore.
>>
>>
>
>This message only showed up in my Inbox today -- nearly 6 months after
>it was sent!
>
>The module you were looking for is cited in the DEPRECATED file in the
>git repo bioperl-live.
>
>Bio::Tools::BPbl2seq          1.5      1.6    use Bio::SearchIO
>
>So I suppose you should try Bio::SearchIO if you are still working on
>this problem.

Yes, it was oddly in the ‘held’ queue on mailman.

chris

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