Re: Cannot download/find BPbl2seq module
2016-05-26 00:09:05 GMT
Sent: Wednesday, May 25, 2016 5:10:35 PM
To: Turnsek, Jernej
Cc: Mark Jensen; Brian Osborne; bioperl-l <at> bioperl.org
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module
On May 25, 2016, at 4:06 PM, Turnsek, Jernej <turnsek <at> fas.harvard.edu> wrote:Thanks everyone for your thoughts and suggestions, especially thanks for the github page with older BioPerl releases. I found this website from winter 07' stating:"Bioperl's older BLAST report parsers - BPlite, BPpsilite, BPbl2seq and Blast.pm - are no longer supported but since legacy Bioperl scripts have been written which use these objects, they are likely to remain within Bioperl for some time."
The error message I see is here:<OAF_error.png>
From: Fields, Christopher J <cjfields <at> illinois.edu>
Sent: Wednesday, May 25, 2016 4:39:28 PM
To: Mark Jensen
Cc: Turnsek, Jernej; bioperl-l <at> bioperl.org
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq moduleOne thing to note: the OAF tools were last released in 2008. There is some possibility that newer versions of bioperl may or may not work with this; if you run into problems I suggest using one of the older releases:chrisOn May 25, 2016, at 2:12 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 present but contains a syntax error.On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <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?"
MarkOn Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <turnsek <at> fas.harvard.edu> wrote: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 .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,
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