[Bioperl-l] problem with bp_genbank2gff.pl

Sat Nov 30 05:08:52 UTC 2013

Re: IGV, I suggest asking the IGV developers at Broad.  They’re fairly responsive and could better answer that question.  I would hazard to guess their support for GFF3 is pretty simple and focused around transcript display, nothing more.

chris

On Nov 29, 2013, at 10:55 PM, Scott Cain <scott at scottcain.net> wrote:

> Also, about your questions (which were buried very deep at the end of the email):
> 
> 1. The script supports a --split option to split GFF from fasta. 
> 
> 2. I don't think there is an option to specifically skip attributes like translation (it shows up in the GFF because it's in the genbank file), but it probably wouldn't be to hard to add that functionality. Patches welcome. 
> 
> 3. I don't know anything about igv. 
> 
> Scott
> 
> 
> Sent from my iPhone
> 
> On Nov 29, 2013, at 3:34 PM, "Fields, Christopher J" <cjfields at illinois.edu> wrote:
> 
>> The latest CPAN release (v 1.6.922) fixes these issues.
>> 
>> chris
>> 
>> On Nov 28, 2013, at 1:08 AM, zhou li <zhouli at tll.org.sg<mailto:zhouli at tll.org.sg>> wrote:
>> 
>> Dear Bioperl people,
>> I am using BioPerl-1.6.1, and the operating system is Mac OS X version 10.8.5.
>> I am trying to convert a local GenBank file to GFF file using bp_genbank2gff.pl, using the following command,
>> $ bp_genbank2gff.pl M21017.gb --stdout > M21017.gff3
>> And I got the following message, I am not sure if this is an error:
>> 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.
>> 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.
>> # 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.
>> 
>> ***************************************************************************
>> And the output file M21017.gff3 is attached.
>> 
>> $head M21017.gff3
>> ##gff-version 3
>> M21017 Genbank region 1 12026 . . . 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
>> M21017 Genbank region 1 12026 . + . ID=Drosophila%20melanogaster;db_xref=taxon%3A7227;mol_type=genomic%20DNA
>> M21017 Genbank gene 1 12026 . + . ID=18S%20rRNA
>> M21017 Genbank RNA 1 7232 . + . ID=18S%20rRNA;note=rRNA%20primary%20transcript
>> M21017 Genbank rRNA 1 1995 . + . ID=18S%20rRNA;product=18S%20ribosomal%20RNA
>> M21017 Genbank gene 2722 2844 . + . ID=5.8S%20rRNA
>> M21017 Genbank rRNA 2722 2844 . + . ID=5.8S%20rRNA;product=5.8S%20ribosomal%20RNA
>> M21017 Genbank gene 2873 2902 . + . ID=2S%20rRNA
>> M21017 Genbank rRNA 2873 2902 . + . ID=2S%20rRNA;product=2S%20ribosomal%20RNA
>> 
>> 
>> When I test another genbank file
>> $ bp_genbank2gff.pl WSSV-AF369029-GenBank.gb --stdout > WSSV-AF369029-GenBank.gff3
>> I also got the error message:
>> 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.
>> 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.
>> $ head WSSV-AF369029-GenBank.gff3
>> ##gff-version 3
>> AF369029 Genbank region 1 292967 . . . ID=AF369029;Alias=AY864671;Note=White%20spot%20syndrome%20virus%2C%20complete%20genome.
>> AF369029 Genbank region 1 292967 . + . ID=White%20spot%20syndrome%20virus;mol_type=genomic%20DNA;isolate=WSSV-TH;country=Thailand;db_xref=taxon%3A342409
>> AF369029 Genbank gene 1 615 . + . ID=VP28;experiment=experimental%20evidence%2C%20no%20additional%20details%20recorded;note=envelope%20protein
>> AF369029 Genbank CDS 1 615 . + . 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
>> AF369029 Genbank CDS 710 2902 . - . 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
>> AF369029 Genbank CDS 3118 4989 . - . Parent=AAK77672.1.t00;codon_start=1;product=ORF3;db_xref=GI%3A15021395;translation=MAWTVMALKDAFTERLVVNKVGSGTDMAPVVEDDRQKSLFQKVENLYRVLVVEQKNSAITLSGNKNTNKRQCRQVEEDKVIFEGEDRTVSNLPQAVKETIAANAESILDYWYKNVIPLLDTKKERSGKSDTFLRTAVICLVRCCVSYKDMKTCSLIYEFEHKILNKSTLDPLLKDILDNKQELLHMDSKYGSKTTSPELAKETIEALYTTVYNHWTNAFKLYQASLTHKPVTGKKYASVIHFIRTWRKIVKAYVSKHNNVERDLSLKNIMKNESADNANVLTIEKMYKKIGNSVKNTNNNSAHQMSDSEDDDDDDDDDCEGMDVCDEASEREKKHQESLYPINTPVTTITGDYIFKVLLELVLSPHIHPEWKIPMCDFVNRNIPKLMKAMETDISNAVIEVRASKVNPVQILPIAANFWDFCKSGKPPSDVKFCMMFNEPSSNETLSSGAGVFGRFIGGPFSHKSKELDIISNCLRSLLLNKEADNLSTRIWREGGSVVCFNYCPITARGAVLGYGEQLSERSIKALWAKKIQDAVTESVKRQRNAADKNSRNCDLLGDEGVVSMKTVTFGCANMLKTQNGMGKFNVVVSFEDSIQANKEGAARQYMSQQVFTHSFPALDQGK
>> 
>> The output file is so tedious, the translation is all showing up. But to me, it is not needed.
>> 1. Is there any way to make the output file more succinct without having the translation included?
>> 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?
>> 3. When I import the WSSV-AF369029-GenBank.gff3 file to IGV, 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?
>> 
>> 
>> 
>> [TLL Conference]<http://conference.tll.org.sg/>
>> 
>> TLL is organizing an international conference on Next Generation Genomic
>> View on Plants, Animals and Microbes on March 5th to 7th, 2014. For more
>> information, please visit http://conference.tll.org.sg<http://conference.tll.org.sg/>
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>> 
>> 
>> Your help is greatly appreciated.
>> Thank you very much!
>> Regards,
>> Zhou Li
>> 
>> 
>> 
>> 
>> <PastedGraphic-1.pdf><M21017.gff3><WSSV-AF369029-GenBank.gff3>
>> 
>> 
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