[Bioperl-l] Cannot download/find BPbl2seq module

Fri May 27 01:44:35 UTC 2016

Ok -- because I am so embarrassed about my lack of historical
BioPerl knowledge, and also about the state of the BioPerl distribution,
I decided to have a look at oaf and see if it could at least use the
latest modules. 

I think it can. In fact, oaf was shipping an instance
of Bio/Tools/Run/StandAloneBlast.pm frozen in time. That was where the
ancient BPbl2seq was used. If you installed it with perl Makefile.PL,
Jernej, you would have written over the version that comes with
BP-1.6.9. 

I pulled the frozen modules out of the original distribution
and MANIFEST, and created https://github.com/majensen/oaf-repackage. I
added hints about where to get the latest versions of the external
tools. I have tried the perl Makefile.PL,... mantra, and I seem to get
something on his test data. 

Do I have time for this? No, but good
Lord, I can't stand the idea of any self-respecting bioinformatician
installing 1.5.2. 

MAJ 

On 2016-05-25 20:09, Turnsek, Jernej wrote:

> Wonderful. I'll give it a shot with v1.5.2 or lower then. 
> 
>
Thank you all again! 
> 
> Jernej 
> 
> -------------------------
> 
>
FROM: Fields, Christopher J 
> 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 
> 
> Yep, those tools used Ian's old BPLite, see here:

> 
>
https://github.com/bioperl/bioperl-live/tree/166d6bf3875e86d78d0d262e134248a47044128d/Bio/Tools
[19] 
> 
> These would last be in the 1.5.2 release series and were
removed prior to v1.6 as their functionality was largely subsumed by
Bio::SearchIO. 
> 
> chris 
> 
>> On May 25, 2016, at 4:06 PM, Turnsek,
Jernej <turnsek at fas.harvard.edu [15]> 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: 
>> 
>> Jernej 
>> -------------------------
>>

>> FROM: Fields, Christopher J <cjfields at illinois.edu [16]>
>> SENT:
Wednesday, May 25, 2016 4:39:28 PM
>> TO: Mark Jensen
>> CC: Turnsek,
Jernej; bioperl-l at bioperl.org [17]
>> 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 [18] 
>> 
>> chris 
>>

>>> On May 25, 2016, at 2:12 PM, Mark A Jensen <maj at fortinbras.us [10]>
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 [11] present but contains a
syntax error. 
>>> On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen
<maj at fortinbras.us [12]> 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 [9]> wrote:

>>>> 
>>>>> Dear BioPerl community, 
>>>>> 
>>>>> I am trying to use
OAF [1] - 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 [2]. 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 [3]). What I tried
to do next is replicate the "my_sequence" example listed on this website
[4] 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 [5] 
>>>>> Department of Systems Biology
| Harvard Medical School 
>>>>> 200 Longwood Ave | Boston, MA 02115

>>>>> (617) 797-5386 | Web [6] | LinkedIn [7] | @SynEnthu [8]
>>>
_______________________________________________
>>> Bioperl-l mailing
list
>>> Bioperl-l at mailman.open-bio.org [13]
>>>
http://mailman.open-bio.org/mailman/listinfo/bioperl-l [14]

Links:
------
[1]
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=
[2]
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=
[3]
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=
[4]
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=
[5]
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=
[6]
https://urldefense.proofpoint.com/v2/url?u=http-3A__openwetware.org_wiki_User-3AJernejTurnsek&d=CwMCAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=lZ-hhOvPCYvc0FKTog464lT_a8U5V5oPA1vGbhdsLf0&s=8xxKVOfN3mHNltU89DhXBRdP1yiZJWcGqB7kDSS4l5Y&e=
[7]
https://urldefense.proofpoint.com/v2/url?u=https-3A__www.linkedin.com_in_jernejt&d=CwMCAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=lZ-hhOvPCYvc0FKTog464lT_a8U5V5oPA1vGbhdsLf0&s=qz_Xb4y07zh10mRuVGhqOpyOFdgIM-o78AKjkiDsNQE&e=
[8]
https://urldefense.proofpoint.com/v2/url?u=https-3A__twitter.com_&d=CwMCAg&c=8hUWFZcy2Z-Za5rBPlktOQ&r=fbHa8Njtvh9VmSnzJxiEUTW9NWDwMMwQAzhgZDO41GQ&m=lZ-hhOvPCYvc0FKTog464lT_a8U5V5oPA1vGbhdsLf0&s=3K__d2ef1qaxPYkO41ROAr3UiLuXDUsz4y7irxULTaY&e=
[9]
mailto:turnsek at fas.harvard.edu
[10] mailto:maj at fortinbras.us
[11]
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=
[12]
mailto:maj at fortinbras.us
[13]
mailto:Bioperl-l at mailman.open-bio.org
[14]
https://urldefense.proofpoint.com/v2/url?u=http-3A__mailman.open-2Dbio.org_mailman_listinfo_bioperl-2Dl&d=CwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=HZh-xFLuhMEYOZH1sjfj31ifO3__xRKf3gjHb4utlnQ&m=Cwy85rCzpHhZv7RSgJP4E6VqPrHGNsjkkPJdYtJs5eU&s=2I-YFf2dUmUY-25k1ENBmJehh2V0SUcvP6yWx-v4Xkk&e=
[15]
mailto:turnsek at fas.harvard.edu
[16] mailto:cjfields at illinois.edu
[17]
mailto:bioperl-l at bioperl.org
[18]
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=
[19]
https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_bioperl_bioperl-2Dlive_tree_166d6bf3875e86d78d0d262e134248a47044128d_Bio_Tools&d=CwMGaQ&c=WO-RGvefibhHBZq3fL85hQ&r=HZh-xFLuhMEYOZH1sjfj31ifO3__xRKf3gjHb4utlnQ&m=G4k_dAxNIMMUw-mo9U5lQCDFiQ8JAp-DpYO0KPqX5Qo&s=fkVjUIuvSbEFwptGko5Ns8oE_35S9TLAyMqk1OyCSrg&e=
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