[Bioperl-l] problem with bp_genbank2gff.pl

Thu Nov 28 09:02:37 UTC 2013

Hi all,
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. In the outputfile,the 8th column is for 'Phase', being any one of 0,1 or 
2, and it is required for CDS features. However, the output file lack 
"phase" for all CDSs. How can I correct this by telling the program do the 
right thing? 
3. 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?
4. When I import the WSSV-AF369029-GenBank.gff3 file to IGV, (see attached 
PastedGraphic-1) 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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