[Bioperl-l] Cannot download/find BPbl2seq module

Wed May 25 21:07:12 UTC 2016

LINK to the website mentioned.<https://classes.soe.ucsc.edu/bme060/Winter07/bptutorial.html>

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________________________________
From: Turnsek, Jernej
Sent: Wednesday, May 25, 2016 5:06 PM
To: Fields, Christopher J; Mark Jensen; Brian Osborne
Cc: bioperl-l at bioperl.org
Subject: Re: [Bioperl-l] Cannot download/find BPbl2seq module

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:

[cid:21e900a8-09f3-4a25-9fb5-63222fa8d638]

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Jernej
________________________________
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 module

One 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:

https://github.com/bioperl/bioperl-live/releases<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl-2Dlive_releases&d=CwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=HZh-xFLuhMEYOZH1sjfj31ifO3__xRKf3gjHb4utlnQ&m=Cwy85rCzpHhZv7RSgJP4E6VqPrHGNsjkkPJdYtJs5eU&s=4jW4FTOSVYIkXWpPG6Zu2F3PNMK80LBl4-4FWQWpbjg&e=>

chris

On May 25, 2016, at 2:12 PM, Mark A Jensen <maj at fortinbras.us<mailto: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<https://urldefense.proofpoint.com/v2/url?u=http-3A__module.is_&d=CwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=HZh-xFLuhMEYOZH1sjfj31ifO3__xRKf3gjHb4utlnQ&m=Cwy85rCzpHhZv7RSgJP4E6VqPrHGNsjkkPJdYtJs5eU&s=gj5zNSf-WpdkMFaCjYr_tQXu5HE6EJx47kbZgkwwOxA&e=> 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__recode.ucc.ie_oaf_&d=CwMCAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=lZ-hhOvPCYvc0FKTog464lT_a8U5V5oPA1vGbhdsLf0&s=xr8pgZ84k-SeZtJZFfR4w1r2siyiqX0a0x45KGAAJl4&e=> - 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ncbi.nlm.nih.gov_pubmed_18384676&d=CwMCAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=lZ-hhOvPCYvc0FKTog464lT_a8U5V5oPA1vGbhdsLf0&s=4046e0aT5FC-dIYsOuh21mcAH8NZrt0prB4mtK8cLwU&e=>. 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<https://urldefense.proofpoint.com/v2/url?u=http-3A__recode.ucc.ie_oaf_download&d=CwMCAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=lZ-hhOvPCYvc0FKTog464lT_a8U5V5oPA1vGbhdsLf0&s=6pghwi61ZeJQUNpLU0SFi_0dGB2AXkMGadYMd-uM5sY&e=>). What I tried to do next is replicate the "my_sequence" example listed on this website<https://urldefense.proofpoint.com/v2/url?u=http-3A__recode.ucc.ie_oaf_download&d=CwMCAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=lZ-hhOvPCYvc0FKTog464lT_a8U5V5oPA1vGbhdsLf0&s=6pghwi61ZeJQUNpLU0SFi_0dGB2AXkMGadYMd-uM5sY&e=> 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://urldefense.proofpoint.com/v2/url?u=https-3A__silver.med.harvard.edu_&d=CwMCAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=lZ-hhOvPCYvc0FKTog464lT_a8U5V5oPA1vGbhdsLf0&s=L1-2LTfJswYKnHzuybKCG2Qtx98LdFG2b3by4FXR7Cg&e=>
Department of Systems Biology | Harvard Medical School
200 Longwood Ave | Boston, MA 02115
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