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<p>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. </p>
<p>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. </p>
<p>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.</p>
<p>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.</p>
<p>MAJ</p>
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<p>On 2016-05-25 20:09, Turnsek, Jernej wrote:</p>
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<p>Wonderful. I'll give it a shot with v1.5.2 or lower then.</p>
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<p>Thank you all again!</p>
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<p><span style="font-size: 12pt;">Jernej</span></p>
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<div id="divRplyFwdMsg" dir="ltr"><span style="font-size: 11pt; color: #000000; font-family: Calibri,sans-serif;"><strong>From:</strong> Fields, Christopher J <br /><strong>Sent:</strong> Wednesday, May 25, 2016 5:10:35 PM<br /><strong>To:</strong> Turnsek, Jernej<br /><strong>Cc:</strong> Mark Jensen; Brian Osborne; bioperl-l@bioperl.org<br /><strong>Subject:</strong> Re: [Bioperl-l] Cannot download/find BPbl2seq module</span>
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<div>Yep, those tools used Ian’s old BPLite, see here:
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<div><a href="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=">https://github.com/bioperl/bioperl-live/tree/166d6bf3875e86d78d0d262e134248a47044128d/Bio/Tools</a></div>
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<div>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.</div>
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<div>chris</div>
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<div>On May 25, 2016, at 4:06 PM, Turnsek, Jernej <<a href="mailto:turnsek@fas.harvard.edu">turnsek@fas.harvard.edu</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;">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:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;"><span>"Bioperl's older BLAST report parsers - BPlite, BPpsilite,<span class="Apple-converted-space"> </span><strong><span style="text-decoration: underline;">BPbl2seq</span></strong><span class="Apple-converted-space"> </span>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."</span></div>
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<div style="margin-top: 0px; margin-bottom: 0px;">The error message I see is here:</div>
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<div style="color: #222222; background-color: #ffffff;">Jernej</div>
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<div id="divRplyFwdMsg" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" dir="ltr"><span style="font-size: 11pt; font-family: Calibri,sans-serif;"><strong>From:</strong><span class="Apple-converted-space"> </span>Fields, Christopher J <<a href="mailto:cjfields@illinois.edu">cjfields@illinois.edu</a>><br /><strong>Sent:</strong><span class="Apple-converted-space"> </span>Wednesday, May 25, 2016 4:39:28 PM<br /><strong>To:</strong><span class="Apple-converted-space"> </span>Mark Jensen<br /><strong>Cc:</strong><span class="Apple-converted-space"> </span>Turnsek, Jernej; <a href="mailto:bioperl-l@bioperl.org"> bioperl-l@bioperl.org</a><br /><strong>Subject:</strong><span class="Apple-converted-space"> </span>Re: [Bioperl-l] Cannot download/find BPbl2seq module</span>
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<div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">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:
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<div><a href="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=">https://github.com/bioperl/bioperl-live/releases</a></div>
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<div>chris</div>
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<div>On May 25, 2016, at 2:12 PM, Mark A Jensen <<a href="mailto:maj@fortinbras.us">maj@fortinbras.us</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Oops, I am wrong about this.<span class="Apple-converted-space"> </span><br /> 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<span class="Apple-converted-space"> </span><a href="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=">module.is</a><span class="Apple-converted-space"> </span>present but contains a syntax error.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;">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?"<br /> Mark</div>
<div class="cm_quote" style="color: #787878;">On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <<a href="mailto:turnsek@fas.harvard.edu">turnsek@fas.harvard.edu</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">Dear <span id="0.9645808873867432" class="highlight" style="background-color: #ffffff;">BioPerl</span><span style="background-color: #ffffff;"> </span>community,</div>
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<div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;">I am trying to use <a href="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=">OAF</a> - 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 <a href="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=">here</a>. I installed Perl (v5.22.2) and <span id="0.2166116948116641" class="highlight" style="background-color: #ffffff;">BioPerl</span> (v1.6.924) which I believe came with HMMER. I haven't installed FASTA and BLAST locally yet - they are both optional (<a href="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=">see this link</a>). What I tried to do next is replicate the "my_sequence" example listed on <a title="http://recode.ucc.ie/oaf/download
Ctrl&#43;Click or tap to follow the link" href="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=">this website</a> using the attached .pl script and .fasta file, but ended up stuck with the error stating I am missing a necessary <span id="0.6919624283748245" class="highlight" style="background-color: #ffffff;">BioPerl</span> module <span style="font-family: Calibri, Arial, Helvetica, sans-serif,;">-<strong><span style="text-decoration: underline;">BPbl2seq</span></strong><span class="Apple-converted-space"> </span>-</span> 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 <span style="font-family: Calibri,Arial,Helvetica,sans-serif,Apple Color Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android Emoji,EmojiSymbols; font-size: x-small;"><span style="font-size: 16px;">BPbl2seq</span></span>. </div>
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<div style="margin-top: 0px; margin-bottom: 0px; font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px;"><span style="font-size: 12pt;">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.</span></div>
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<div style="margin-top: 0px; margin-bottom: 0px;">Thank you and kind regards,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;">Jernej Turnsek</div>
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<div><span style="color: #222222;"><span style="font-family: Arial; font-size: xx-small;"><strong>Jernej Turnsek </strong></span></span></div>
<div style="font-size: small;"><span style="font-family: Arial; font-size: x-small;"><span style="color: #222222;">Ph.D. Candidate |<span class="Apple-converted-space"> </span></span><a id="LPNoLP" href="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="><span style="color: #0000ff;">Pamela Silver's Lab </span></a></span></div>
<div style="font-size: small;"><span style="font-size: x-small; color: #222222;"><span style="font-family: Arial;">Department of Systems Biology | Harvard Medical School</span></span></div>
<div style="font-size: small;"><span style="font-size: x-small; color: #222222;"><span style="font-family: Arial;">200 Longwood Ave | Boston, MA 02115</span></span></div>
<div style="font-size: small;"><span style="font-family: Arial; font-size: xx-small;"><span style="color: #222222;">(617) 797-5386 |<span class="Apple-converted-space"> </span></span><a id="LPNoLP" href="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="><span style="color: #0000ff;">Web</span></a><span style="color: #222222;"><span class="Apple-converted-space"> </span>|<span class="Apple-converted-space"> </span></span></span><span style="font-family: Arial; font-size: x-small;"><a id="LPNoLP" href="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="><span style="color: #0000ff;">LinkedIn</span></a> </span><span style="font-family: Arial; font-size: x-small;">|<span class="Apple-converted-space"> </span><span style="color: #0000ff;"><a id="LPNoLP" href="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=">@SynEnthu</a></span></span></div>
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