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<p>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:</p>
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<p><span style="font-family: 'Times New Roman';">"Bioperl's older BLAST report parsers - BPlite, BPpsilite,
<b><u>BPbl2seq</u></b> 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><br>
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<p>The error message I see is here:</p>
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<div style="color:rgb(34,34,34); background-color:rgb(255,255,255)">Jernej</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Fields, Christopher J <cjfields@illinois.edu><br>
<b>Sent:</b> Wednesday, May 25, 2016 4:39:28 PM<br>
<b>To:</b> Mark Jensen<br>
<b>Cc:</b> Turnsek, Jernej; bioperl-l@bioperl.org<br>
<b>Subject:</b> Re: [Bioperl-l] Cannot download/find BPbl2seq module</font>
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<div>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 class=""><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=" class="">https://github.com/bioperl/bioperl-live/releases</a></div>
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<div class="">chris</div>
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<div class="">On May 25, 2016, at 2:12 PM, Mark A Jensen <<a href="mailto:maj@fortinbras.us" class="">maj@fortinbras.us</a>> wrote:</div>
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Oops, I am wrong about this.<span class="Apple-converted-space"> </span><br class="">
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=" class="">module.is</a><span class="Apple-converted-space"> </span>present
but contains a syntax error.</p>
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On Wed, May 25, 2016 at 2:45 PM, Mark A Jensen <<a href="mailto:maj@fortinbras.us" class="">maj@fortinbras.us</a>> wrote:</div>
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<p dir="ltr" class="">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 class="">
Mark</p>
<div class="cm_quote" style="color: rgb(120, 120, 120);">On Wed, May 25, 2016 at 1:21 PM, Turnsek, Jernej <<a href="mailto:turnsek@fas.harvard.edu" class="">turnsek@fas.harvard.edu</a>> wrote:</div>
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Dear <span class="highlight" id="0.9645808873867432" style="background-color: rgb(255, 255, 255);">BioPerl</span><span style="background-color: rgb(255, 255, 255);" class=""> </span>community,</p>
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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=" class="">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=" class="">here</a>. I
installed Perl (v5.22.2) and <span class="highlight" id="0.2166116948116641" style="background-color: rgb(255, 255, 255);">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=" class="">see
this link</a>). What I tried to do next is replicate the "my_sequence" example listed on <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=" title="http://recode.ucc.ie/oaf/download
Ctrl+Click or tap to follow the link" class="">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 class="highlight" id="0.6919624283748245" style="background-color: rgb(255, 255, 255);">BioPerl</span> module <span style="font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols;" class="">-<b class=""><u class="">BPbl2seq</u></b><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 <font face="Calibri,Arial,Helvetica,sans-serif,Apple Color
Emoji,Segoe UI Emoji,NotoColorEmoji,Segoe UI Symbol,Android
Emoji,EmojiSymbols" size="2" class=""><span style="font-size: 16px;" class="">BPbl2seq</span></font>. </p>
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<span style="font-size: 12pt;" class="">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></p>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I look forward to hearing from you.<br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Thank you and kind regards,<br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Jernej Turnsek</div>
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<div class=""><span style="color: rgb(34, 34, 34);" class=""><font size="1" face="Arial" class=""><b class="">Jernej Turnsek </b></font></span></div>
<div style="font-size: small;" class=""><span style="font-family: Arial; font-size: x-small;" class=""><font color="#222222" class="">Ph.D. Candidate |<span class="Apple-converted-space"> </span></font><a 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=" id="LPNoLP" class=""><font color="#0000ff" class="">Pamela
Silver's Lab </font></a></span></div>
<div style="font-size: small;" class=""><span style="font-size: x-small; color: rgb(34, 34, 34);" class=""><font face="Arial" class="">Department of Systems Biology | Harvard Medical School</font></span></div>
<div style="font-size: small;" class=""><span style="font-size: x-small; color: rgb(34, 34, 34);" class=""><font face="Arial" class="">200 Longwood Ave | Boston, MA 02115</font></span></div>
<div style="font-size: small;" class=""><font size="1" style="font-family: Arial;" class=""><font color="#222222" class="">(617) 797-5386 |<span class="Apple-converted-space"> </span></font><a 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=" id="LPNoLP" class=""><font color="#0000ff" class="">Web</font></a><font color="#222222" class=""><span class="Apple-converted-space"> </span>|<span class="Apple-converted-space"> </span></font></font><span style="font-family: Arial; font-size: x-small;" class=""><a 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=" id="LPNoLP" class=""><font color="#0000ff" class="">LinkedIn</font></a> </span><span style="font-family: Arial; font-size: x-small;" class="">|<span class="Apple-converted-space"> </span><font color="#0000ff" class=""><a 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=" id="LPNoLP" class="">@SynEnthu</a></font></span></div>
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mailing list</span><br 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;" class="">
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