<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Thanks I’ll update the related scripts. In my tests the old regular expression still works, but ends up adding the OX= tag as part of the GFF3 entry and not throwing a hash ref error. So you still may have another issue if you are getting a hash ref error.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Mar 14, 2020, at 11:24 AM, Christopher Keeling <<a href="mailto:christopher.keeling.1@ulaval.ca" class="">christopher.keeling.1@ulaval.ca</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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Hello,
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<div class="">In sub parse_blast{, during parsing of uniprot fasta file:
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<div class="">if (/>(\S+)\s+(.*?)\s+OS=(.*?)\s+(GN=(.*?)\s+)?PE=/) {</div>
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</div>
<div class="">should be changed to:</div>
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</div>
<div class="">if (/>sp\|(\S+)\|\S+\s+(.*?)\s+OS=(.*?)\s+OX=\S+\s+(GN=(.*?)\s+)?PE=/) {</div>
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</div>
<div class="">to avoid "Can't use string ("") as a HASH ref while "strict refs" in use at…" errors.</div>
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<div class="">For UniProt release 2020_01: <a href="ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz" class="">
ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz</a></div>
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<div class="">Cheers,</div>
<div class="">Chris<br class="">
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<div style="caret-color: rgb(0, 0, 0); font-size: 16px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; font-family: LucidaGrande;" class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">
<b class=""><span lang="FR-CA" style="font-size: 12pt; font-family: "AvantGarde Bk BT"; color: gray;" class=""><br class="Apple-interchange-newline">
<br class="Apple-interchange-newline">
--<br class="">
Christopher I. Keeling</span></b><span lang="FR-CA" style="font-size: 12pt; font-family: "AvantGarde Bk BT"; color: gray;" class=""><br class="">
</span><i class=""><span lang="FR-CA" style="font-size: 10pt; font-family: "AvantGarde Bk BT"; color: gray;" class="">Chercheur scientifique en génomique forestière/ Research Scientist in Forest Genomics</span></i><span style="color: rgb(31, 73, 125);" class=""><o:p class=""></o:p></span></div><p class="MsoNormal" style="margin: 0cm 0cm 12pt; font-size: 11pt; font-family: Calibri, sans-serif;">
<span lang="FR-CA" style="font-family: "AvantGarde Bk BT"; color: gray;" class=""><br class="">
</span><b class=""><span lang="FR-CA" style="font-size: 10pt; font-family: "AvantGarde Bk BT"; color: gray;" class="">Ressources naturelles Canada / Natural Resources Canada<br class="">
Service canadien des forêts / Canadian Forest Service<br class="">
Centre de foresterie des Laurentides / Laurentian Forestry Centre<br class="">
1055, rue du PEPS Québec, QC G1V 4C7 Canada<br class="">
<a href="https://cfs.nrcan.gc.ca/employees/read/ckeeling" style="color: rgb(149, 79, 114);" class="">https://cfs.nrcan.gc.ca/employees/read/ckeeling</a><br class="">
<br class="">
Professeur associé<br class="">
Département de biochimie, de microbiologie et de bio-informatique<br class="">
Université Laval<br class="">
<a href="https://www.researchgate.net/profile/Christopher_Keeling" style="color: rgb(149, 79, 114);" class="">https://www.researchgate.net/profile/Christopher_Keeling</a><br class="">
<a href="https://scholar.google.ca/citations?user=KtGr86UAAAAJ" style="color: rgb(149, 79, 114);" class="">https://scholar.google.ca/citations?user=KtGr86UAAAAJ</a><o:p class=""></o:p></span></b></p>
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<span style="color: rgb(31, 73, 125);" class=""> </span></div>
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