[Bioperl-l] problem with bp_genbank2gff.pl

Thu Nov 28 02:08:15 EST 2013

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?

Your help is greatly appreciated.
Thank you very much!
Regards,
Zhou Li

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