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Hi Carson,
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<div class="">I’m now using Maker 3.01.03, and I’m finding that maker_functional_gff and maker_functional_fasta still are not behaving as they should. I’m getting an error:</div>
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<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">Can't use string ("") as a HASH ref while "strict refs" in use at /usr/local/bin/maker/bin/maker_functional_gff line 55, <$IN> line 167.</span></div>
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<div class="">Version 2020_03 of uniprot_sprot.fasta starts like this:</div>
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<div class="">>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) OX=654924 GN=FV3-001R PE=4 SV=1</div>
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<div class="">Based on your scripts, this is the example of your first condition. However, I find that I need to change it (in red) to get it to work as I understand it should work:</div>
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<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> #>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) OX=654924 GN=FV3-001R PE=4 SV=1</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures;" class=""><span class="Apple-tab-span" style="color: rgb(57, 53, 51); white-space: pre;"></span><font color="#393533" class="">if (/></font><font color="#ff2600" class="">sp\|(\S+)\|\S+</font><font color="#393533" class="">\s+(.*?)\s+OS=(.*?)\s+OX=</font><font color="#ff2600" class="">\S+</font><font color="#393533" class="">\s+(GN=(.*?)\s+)?PE=/)
{</font></span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> $id = $1;</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> $desc = $2;</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> $org = $3;</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures;" class=""><font color="#393533" class=""> $name =
</font><font color="#ff2600" class="">$5</font><font color="#393533" class=""> || ‘';</font></span></div>
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<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""><span class="Apple-tab-span" style="white-space:pre"></span>}</span></div>
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</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Compared to what is in </span>3.01.03:</div>
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<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> #>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) OX=654924 GN=FV3-001R PE=4 SV=1</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> if (/>(\S+)\s+(.*?)\s+OS=(.*?)\s+OX=(.*?)\s+(GN=(.*?)\s+)?PE=/) {</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class=""> $id = $1;</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> $desc = $2;</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> $org = $3;</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> $name = $6 || '';</span></div>
<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class=""> }</span></div>
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<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Thus, </span>with my edits:</div>
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<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; background-color: rgb(245, 245, 245);" class="">
<span style="color: rgb(57, 53, 51); font-variant-ligatures: no-common-ligatures;" class="">>sp|Q62559|IFT52_MOUSE Intraflagellar transport protein 52 homolog OS=Mus musculus OX=10090 GN=</span><span style="font-variant-ligatures: no-common-ligatures;" class=""><font color="#393532" class="">Ift52</font></span><span style="color: rgb(57, 53, 51); font-variant-ligatures: no-common-ligatures;" class="">
PE=1 SV=2</span></div>
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<div class="">maker_functional_gff would result in:</div>
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<div style="margin: 0px; font-stretch: normal; font-size: 14px; line-height: normal; font-family: Menlo; color: rgb(57, 53, 51); background-color: rgb(245, 245, 245);" class="">
<span style="font-variant-ligatures: no-common-ligatures" class="">...Note=Similar to Ift52: Intraflagellar transport protein 52 homolog (Mus musculus);</span></div>
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</span></div>
<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">And maker_function_gff would result in:</span></div>
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<span style="font-variant-ligatures: no-common-ligatures" class="">Name:"Similar to
</span><span style="font-variant-ligatures: no-common-ligatures; color: #f13128" class=""><b class="">Ift52</b></span><span style="font-variant-ligatures: no-common-ligatures" class=""> Intraflagellar transport protein 52 homolog (Mus musculus)"</span></div>
</span></div>
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<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Are these the expected behaviours?</span></div>
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<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Cheers,</span></div>
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<div class=""><span style="font-variant-ligatures: no-common-ligatures" class="">Chris</span></div>
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<blockquote type="cite" class="">
<div class="">On Mar 14, 2020, at 1:24 PM, Christopher Keeling <<a href="mailto:christopher.keeling.1@ulaval.ca" class="">christopher.keeling.1@ulaval.ca</a>> wrote:</div>
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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 class="">should be changed to:</div>
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<div class="">if (/>sp\|(\S+)\|\S+\s+(.*?)\s+OS=(.*?)\s+OX=\S+\s+(GN=(.*?)\s+)?PE=/) {</div>
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<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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