<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Bioperl people,<div>I am using BioPerl-1.6.1, and the operating system is Mac OS X version 10.8.5.</div><div>I am trying to convert a local GenBank file to GFF file using bp_genbank2gff.pl, using the following command,</div><div><font color="#00a3d7">$ bp_genbank2gff.pl M21017.gb --stdout > M21017.gff3</font></div><div>And I got the following message, I am not sure if this is an error:</div><div><div><font color="#e32400">Replacement list is longer than search list at /Users/zhouli/perl5/perlbrew/perls/perl-5.18.1/lib/site_perl/5.18.1/Bio/Range.pm line 251.</font></div><div><font color="#e32400">UNIVERSAL->import is deprecated and will be removed in a future perl at /Users/zhouli/perl5/perlbrew/perls/perl-5.18.1/lib/site_perl/5.18.1/Bio/Tree/TreeFunctionsI.pm line 94.</font></div></div><div><div><font color="#e32400"># working on region:M21017, Drosophila melanogaster, 09-MAY-1994, D.melanogaster 18S, 5.8S 2S and 28S rRNA genes, complete, and 18S rRNA gene, 5' end, clone pDm238.</font></div><div><br></div></div><div>***************************************************************************</div><div>And the output file M21017.gff3 is attached.</div><div><br></div><div><font color="#00a3d7">$head M21017.gff3</font></div><div><div>##gff-version 3</div><div>M21017<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>region<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>12026<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=M21017;Note=D.melanogaster%2018S%2C%205.8S%202S%20and%2028S%20rRNA%20genes%2C%20complete%2C%20and%2018S%20rRNA%20gene%2C%205%27%20end%2C%20clone%20pDm238.;Alias=M29800</div><div>M21017<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>region<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>12026<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=Drosophila%20melanogaster;db_xref=taxon%3A7227;mol_type=genomic%20DNA</div><div>M21017<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>gene<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>12026<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=18S%20rRNA</div><div>M21017<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>RNA<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>7232<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=18S%20rRNA;note=rRNA%20primary%20transcript</div><div>M21017<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>rRNA<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>1995<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=18S%20rRNA;product=18S%20ribosomal%20RNA</div><div>M21017<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>gene<span class="Apple-tab-span" style="white-space:pre"> </span>2722<span class="Apple-tab-span" style="white-space:pre"> </span>2844<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=5.8S%20rRNA</div><div>M21017<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>rRNA<span class="Apple-tab-span" style="white-space:pre"> </span>2722<span class="Apple-tab-span" style="white-space:pre"> </span>2844<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=5.8S%20rRNA;product=5.8S%20ribosomal%20RNA</div><div>M21017<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>gene<span class="Apple-tab-span" style="white-space:pre"> </span>2873<span class="Apple-tab-span" style="white-space:pre"> </span>2902<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=2S%20rRNA</div><div>M21017<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>rRNA<span class="Apple-tab-span" style="white-space:pre"> </span>2873<span class="Apple-tab-span" style="white-space:pre"> </span>2902<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=2S%20rRNA;product=2S%20ribosomal%20RNA</div></div><div><br></div><div><br></div><div>When I test another genbank file </div><div><font color="#008cb4">$ bp_genbank2gff.pl WSSV-AF369029-GenBank.gb --stdout > WSSV-AF369029-GenBank.gff3 </font></div><div>I also got the error message:</div><div><div><font color="#b51a00">Replacement list is longer than search list at /Users/zhouli/perl5/perlbrew/perls/perl-5.18.1/lib/site_perl/5.18.1/Bio/Range.pm line 251.</font></div><div><font color="#b51a00">UNIVERSAL->import is deprecated and will be removed in a future perl at /Users/zhouli/perl5/perlbrew/perls/perl-5.18.1/lib/site_perl/5.18.1/Bio/Tree/TreeFunctionsI.pm line 94.</font></div></div><div><div><font color="#008cb4">$ head WSSV-AF369029-GenBank.gff3</font></div><div>##gff-version 3</div><div>AF369029<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>region<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>292967<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=AF369029;Alias=AY864671;Note=White%20spot%20syndrome%20virus%2C%20complete%20genome.</div><div>AF369029<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>region<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>292967<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=White%20spot%20syndrome%20virus;mol_type=genomic%20DNA;isolate=WSSV-TH;country=Thailand;db_xref=taxon%3A342409</div><div>AF369029<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>gene<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>615<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>ID=VP28;experiment=experimental%20evidence%2C%20no%20additional%20details%20recorded;note=envelope%20protein</div><div>AF369029<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>1<span class="Apple-tab-span" style="white-space:pre"> </span>615<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>+<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=VP28.t00;translation=MDLSFTLSVVSAILAITAVIAVFIVIFRYHNTVTKTIETHTDNIETNMDENLRIPVTAEVGSGYFKMTDVSFDSDTLGKIKIRNGKSDAQMKEEDADLVITPVEGRALEVTVGQNLTFEGTFKVWNNTSRKINITGMQMVPKINPSKAFVGSSNTSSFTPVSIDEDEVGTFVCGTTFGAPIAATAGGNLFDMYVHVTYSGTETE;db_xref=GI%3A15021393;protein_id=AAK77670.1;product=ORF1%2C%20VP28%2C%20gene%20family%201;note=envelope%20protein;codon_start=1</div><div>AF369029<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>710<span class="Apple-tab-span" style="white-space:pre"> </span>2902<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=AAK77671.1.t00;translation=MEGGDQRTKLTPATVMGLYQSKTPGEGEGGEGGGQFKIPSAIAVKSCCSKNATRRSPPSDSPYSLRPMKRLKKNNGEVGGKAPPPVTLRLREDYESTPYNFNRNKKKRPITIDENQFATLNPTYATDIIKKQQLPSVSAASVLRKHRANADTQYRKRFSHPNCAKFSTVNLKARDYTPLSVLRSHVKGPKHLKSSCDTVTETNVVKRNFSSIDKWVKLEKPPCYFAVAEADTNIAAGLESPFHLIRQAAKLGLISDVQDVSSNYETIKQSCIDAKEKASKFLWSNNRTKQPPSSWWPVGFGSKNLSVLDTSPLLNWNRLCKNNGKGWIKTMSIDHMAKNVFKLSPGACESILEKKTTLLGEVTAQCKKWESYRRNIPVPAHVQPEYASQVVMIGPSELYLEVKVGVYYMLETGKVIKFMTDKEMYCEFVFETVFSHALEGRMKGAVGVRKMCVEGFCVEMDFAGISVIDVLNGDLKCKMDENVVQQPNPSTTSSKPAAELMQDHGSLCRMRDTLYGVRMLQATGRLPEGLQSKCKKPITDSISAIAIVGKMRERMLNQLPFVLVEIVNIVTRLSQQGLVNPDIKSDNIVIDGITGQPKMIDFGLIVPCKKYYNFKCWGTDERFFSNHPHTAPEFINSELCSETAMTFGLAYLLIDMLSILIKRTADLSANSIYTNIPFLSIVSKMYDQEKTNRPRAYEIAPVIGACFPFKDNIAKLFQSPKHSLYSKKVK;db_xref=GI%3A15021394;codon_start=1;product=ORF2%2C%20putative%20serine%2Fthreonine%20protein%20kinase%20%28PK1%29%2C%20gene%20family%202</div><div>AF369029<span class="Apple-tab-span" style="white-space:pre"> </span>Genbank<span class="Apple-tab-span" style="white-space:pre"> </span>CDS<span class="Apple-tab-span" style="white-space:pre"> </span>3118<span class="Apple-tab-span" style="white-space:pre"> </span>4989<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>-<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Parent=AAK77672.1.t00;codon_start=1;product=ORF3;db_xref=GI%3A15021395;translation=MAWTVMALKDAFTERLVVNKVGSGTDMAPVVEDDRQKSLFQKVENLYRVLVVEQKNSAITLSGNKNTNKRQCRQVEEDKVIFEGEDRTVSNLPQAVKETIAANAESILDYWYKNVIPLLDTKKERSGKSDTFLRTAVICLVRCCVSYKDMKTCSLIYEFEHKILNKSTLDPLLKDILDNKQELLHMDSKYGSKTTSPELAKETIEALYTTVYNHWTNAFKLYQASLTHKPVTGKKYASVIHFIRTWRKIVKAYVSKHNNVERDLSLKNIMKNESADNANVLTIEKMYKKIGNSVKNTNNNSAHQMSDSEDDDDDDDDDCEGMDVCDEASEREKKHQESLYPINTPVTTITGDYIFKVLLELVLSPHIHPEWKIPMCDFVNRNIPKLMKAMETDISNAVIEVRASKVNPVQILPIAANFWDFCKSGKPPSDVKFCMMFNEPSSNETLSSGAGVFGRFIGGPFSHKSKELDIISNCLRSLLLNKEADNLSTRIWREGGSVVCFNYCPITARGAVLGYGEQLSERSIKALWAKKIQDAVTESVKRQRNAADKNSRNCDLLGDEGVVSMKTVTFGCANMLKTQNGMGKFNVVVSFEDSIQANKEGAARQYMSQQVFTHSFPALDQGK</div></div><div><br></div><div>The output file is so tedious, the translation is all showing up. But to me, it is not needed.</div><div>1. Is there any way to make the output file more succinct without having the translation included?</div><div>2. Also, is there any way to split the output file to two files, one is the GFF3 file and the other one is DNA fasta sequence file?</div><div>3. When I import the <span style="color: rgb(0, 140, 180); ">WSSV-AF369029-GenBank.gff3 file to IGV, </span>it displays the protein ID if there is no gene name for the sequence, e.g. those with feature "CDS" display the protein ID, and those with feature "gene" display gene ID, is this the way it works? I want to display the ORF ID, what should I do?</div><div> </div><div></div>
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