Re: Cannot download/find BPbl2seq module
"Mark A. Jensen" <[email protected]> Thu, 26 May 2016 21:44:35 -0400
| Newsgroups | gmane.comp.lang.perl.bio.general |
|---|---|
| Message-ID | <[email protected]> |
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; [email protected] > 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 <[email protected] [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 <[email protected] [16]> >> SENT: Wednesday, May 25, 2016 4:39:28 PM >> TO: Mark Jensen >> CC: Turnsek, Jernej; [email protected] [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 <[email protected] [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 <[email protected] [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 <[email protected] [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 >>> [email protected] [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:[email protected] [10] mailto:[email protected] [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:[email protected] [13] mailto:[email protected] [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:[email protected] [16] mailto:[email protected] [17] mailto:[email protected] [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= _______________________________________________ Bioperl-l mailing list [email protected] http://mailman.open-bio.org/mailman/listinfo/bioperl-l