Genbank Parsing Problem?

[mercutio22]

Hi Brad, AnnotationSketch is complaining about the parsed file again:

GenomeTools error: CDS feature on line 27 in file "../../mirna-django/src/scripts/tp53.gff3" has the wrong phase 0 (should be 1)

I don't know if the problem is with their GFF3 parser though. Can you tell me what you think?

http://paste.debian.net/159462/

[chapmanb]

Hugo; I think that the phase is correct but happy to adjust if the GenomeTools folks think otherwise. The GFF spec specifies the phase as 0,1 or 2:

http://www.sequenceontology.org/gff3.shtml

while codon_start from the GenBank file is 1, 2 or 3:

http://www.ddbj.nig.ac.jp/FT/full_index.html#7.2

so I've made the adjustment from 1 to 0 in the GFF output when converting. Let me know if your interaction with the GenomeTools developers indicate I've missed something in the conversion.

[mercutio22]

Thanks Brad. I will contact them and will let you know asap.

 .''.      Hugo A. M. Torres : :' : . '   “Talk is cheap,  -    show me the code. ”  -- L. Torvalds.

On Mon, Mar 12, 2012 at 3:04 PM, Brad Chapman reply@reply.github.com wrote:

Hugo; I think that the phase is correct but happy to adjust if the GenomeTools folks think otherwise. The GFF spec specifies the phase as 0,1 or 2:

http://www.sequenceontology.org/gff3.shtml

while codon_start from the GenBank file is 1, 2 or 3:

http://www.ddbj.nig.ac.jp/FT/full_index.html#7.2

so I've made the adjustment from 1 to 0 in the GFF output when converting. Let me know if your interaction with the GenomeTools developers indicate I've missed something in the conversion.

---

Reply to this email directly or view it on GitHub: https://github.com/chapmanb/bcbb/issues/52#issuecomment-4457847

[mercutio22]

HI Brad, perhaps this might be useful for testing your program: http://modencode.oicr.on.ca/cgi-bin/validate_gff3_online

I tried and the tool pointed for instance is that the produced gff3 file file has a "source" field. IIRC Peter Cock in one his blog posts says genbank has those but GFF3 does not.

Here, I paste you a sample report:

GFF3 File Validation Report

ontology_file(s):

http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo

generated: 12-Mar-12 15:27:10

###############################################################################

THIS FILE HAS NOT BEEN VALIDATED, IT CONTAINS ERRORS, PLEASE REVIEW REPORT!

(NO WARNINGS HAVE BEEN ISSUED FOR THIS FILE)

###############################################################################

###############################################################################

THIS FILE HAS BEEN PROCESSED ENTIRELY AND ALL ERRORS/WARNINGS ARE REPORTED!

###############################################################################

First 10 lines of the analyzed GFF3 file follows:

# [line 1]> ##gff-version 3 [line 2]> ##sequence-region NG_017013.1 1 26144 [line 3]> NG_017013.1 annotation remark 1 26144 .
[line 3]> . . comment=REVIEWED%20REFSEQ%3A%20This%20record%20has%20been%20curated%20by%20NCBI%20staff%20in%0Acollaboration%20with%20Graham%20Taylor.%20The%20reference%20sequence%20was%0Aderived%20from%20AC087388.9%20and%20AC007421.13.%0AThis%20sequence%20is%20a%20reference%20standard%20in%20the%20RefSeqGene%20project.%0APublication%20Note%3A%20%20This%20RefSeq%20record%20includes%20a%20subset%20of%20the%0Apublications%20that%20are%20available%20for%20this%20gene.%20Please%20see%20the%20Gene%0Arecord%20to%20access%20additional%20publications.%0ASummary%3A%20This%20gene%20encodes%20tumor%20protein%20p53%2C%20which%20responds%20to%0Adiverse%20cellular%20stresses%20to%20regulate%20target%20genes%20that%20induce%20cell%0Acycle%20arrest%2C%20apoptosis%2C%20senescence%2C%20DNA%20repair%2C%20or%20changes%20in%0Ametabolism.%20p53%20protein%20is%20expressed%20at%20low%20level%20in%20normal%20cells%0Aand%20at%20a%20high%20level%20in%20a%20variety%20of%20transformed%20cell%20lines%2C%20where%0Ait%27s%20believed%20to%20contribute%20to%20transformation%20and%20malignancy.%20p53%0Ais%20a%20DNA-binding%20protein%20containing%20transcription%20activation%2C%0ADNA-binding%2C%20and%20oligomerization%20domains.%20It%20is%20postulated%20to%20bind%0Ato%20a%20p53-binding%20site%20and%20activate%20expression%20of%20downstream%20genes%0Athat%20inhibit%20growth%20and/or%20invasion%2C%20and%20thus%20function%20as%20a%20tumor%0Asuppressor.%20Mutants%20of%20p53%20that%20frequently%20occur%20in%20a%20number%20of%0Adifferent%20human%20cancers%20fail%20to%20bind%20the%20consensus%20DNA%20binding%0Asite%2C%20and%20hence%20cause%20the%20loss%20of%20tumor%20suppressor%20activity.%0AAlterations%20of%20this%20gene%20occur%20not%20only%20as%20somatic%20mutations%20in%0Ahuman%20malignancies%2C%20but%20also%20as%20germline%20mutations%20in%20some%0Acancer-prone%20families%20with%20Li-Fraumeni%20syndrome.%20Multiple%20p53%0Avariants%20due%20to%20alternative%20promoters%20and%20multiple%20alternative%0Asplicing%20have%20been%20found.%20These%20variants%20encode%20distinct%20isoforms%2C%0Awhich%20can%20regulate%20p53%20transcriptional%20activity.%20%5Bprovided%20by%0ARefSeq%2C%20Jul%202008%5D.; [line 3]> sequence_version=1;source=Homo%20sapiens%20%28human%29; [line 3]> taxonomy=Eukaryota,Metazoa,Chordata, [line 3]> Craniata,Vertebrata,Euteleostomi, [line 3]> Mammalia,Eutheria,Euarchontoglires, [line 3]> Primates,Haplorrhini,Catarrhini, [line 3]> Hominidae,Homo;keywords=RefSeqGene; [line 3]> references=location%3A%20%5B0%3A26144%5D%0Aauthors%3A%20Marcel%2CV.%2C%20Tran%2CP.L.%2C%20Sagne%2CC.%2C%20Martel-Planche%2CG.%2C%20Vaslin%2CL.%2C%20Teulade-Fichou%2CM.P.%2C%20Hall%2CJ.%2C%20Mergny%2CJ.L.%2C%20Hainaut%2CP.%20and%20Van%20Dyck%2CE.%0Atitle%3A%20G-quadruplex%20structures%20in%20TP53%20intron%203%3A%20role%20in%20alternative%20splicing%20and%20in%20production%20of%20p53%20mRNA%20isoforms%0Ajournal%3A%20Carcinogenesis%2032%20%283%29%2C%20271-278%20%282011%29%0Amedline%20id%3A%20%0Apubmed%20id%3A%2021112961%0Acomment%3A, [line 3]> location%3A%20%5B0%3A26144%5D%0Aauthors%3A%20Naidu%2CS.R.%2C%20Love%2CI.M.%2C%20Imbalzano%2CA.N.%2C%20Grossman%2CS.R.%20and%20Androphy%2CE.J.%0Atitle%3A%20The%20SWI/SNF%20chromatin%20remodeling%20subunit%20BRG1%20is%20a%20critical%20regulator%20of%20p53%20necessary%20for%20proliferation%20of%20malignant%20cells%0Ajournal%3A%20Oncogene%2028%20%2827%29%2C%202492-2501%20%282009%29%0Amedline%20id%3A%20%0Apubmed%20id%3A%2019448667%0Acomment%3A, [line 3]> location%3A%20%5B0%3A26144%5D%0Aauthors%3A%20Anczukow%2CO.%2C%20Ware%2CM.D.%2C%20Buisson%2CM.%2C%20Zetoune%2CA.B.%2C%20Stoppa-Lyonnet%2CD.%2C%20Sinilnikova%2CO.M.%20and%20Mazoyer%2CS.%0Atitle%3A%20Does%20the%20nonsense-mediated%20mRNA%20decay%20mechanism%20prevent%20the%20synthesis%20of%20truncated%20BRCA1%2C%20CHK2%2C%20and%20p53%20proteins%3F%0Ajournal%3A%20Hum.%20Mutat.%2029%20%281%29%2C%2065-73%20%282008%29%0Amedline%20id%3A%20%0Apubmed%20id%3A%2017694537%0Acomment%3A, [line 3]> location%3A%20%5B0%3A26144%5D%0Aauthors%3A%20Bourdon%2CJ.C.%0Atitle%3A%20p53%20Family%20isoforms%0Ajournal%3A%20Curr%20Pharm%20Biotechnol%208%20%286%29%2C%20332-336%20%282007%29%0Amedline%20id%3A%20%0Apubmed%20id%3A%2018289041%0Acomment%3A%20Review%20article, [line 3]> location%3A%20%5B0%3A26144%5D%0Aauthors%3A%20Murray-Zmijewski%2CF.%2C%20Lane%2CD.P.%20and%20Bourdon%2CJ.C.%0Atitle%3A%20p53/p63/p73%20isoforms%3A%20an%20orchestra%20of%20isoforms%20to%20harmonise%20cell%20differentiation%20and%20response%20to%20stress%0Ajournal%3A%20Cell%20Death%20Differ.%2013%20%286%29%2C%20962-972%20%282006%29%0Amedline%20id%3A%20%0Apubmed%20id%3A%2016601753%0Acomment%3A%20Review%20article, [line 3]> location%3A%20%5B0%3A26144%5D%0Aauthors%3A%20Flaman%2CJ.M.%2C%20Waridel%2CF.%2C%20Estreicher%2CA.%2C%20Vannier%2CA.%2C%20Limacher%2CJ.M.%2C%20Gilbert%2CD.%2C%20Iggo%2CR.%20and%20Frebourg%2CT.%0Atitle%3A%20The%20human%20tumour%20suppressor%20gene%20p53%20is%20alternatively%20spliced%20in%20normal%20cells%0Ajournal%3A%20Oncogene%2012%20%284%29%2C%20813-818%20%281996%29%0Amedline%20id%3A%20%0Apubmed%20id%3A%208632903%0Acomment%3A, [line 3]> location%3A%20%5B0%3A26144%5D%0Aauthors%3A%20Lamb%2CP.%20and%20Crawford%2CL.%0Atitle%3A%20Characterization%20of%20the%20human%20p53%20gene%0Ajournal%3A%20Mol.%20Cell.%20Biol.%206%20%285%29%2C%201379-1385%20%281986%29%0Amedline%20id%3A%20%0Apubmed%20id%3A%202946935%0Acomment%3A, [line 3]> location%3A%20%5B0%3A26144%5D%0Aauthors%3A%20Harlow%2CE.%2C%20Williamson%2CN.M.%2C%20Ralston%2CR.%2C%20Helfman%2CD.M.%20and%20Adams%2CT.E.%0Atitle%3A%20Molecular%20cloning%20and%20in%20vitro%20expression%20of%20a%20cDNA%20clone%20for%20human%20cellular%20tumor%20antigen%20p53%0Ajournal%3A%20Mol.%20Cell.%20Biol.%205%20%287%29%2C%201601-1610%20%281985%29%0Amedline%20id%3A%20%0Apubmed%20id%3A%203894933%0Acomment%3A, [line 3]> location%3A%20%5B0%3A26144%5D%0Aauthors%3A%20Zakut-Houri%2CR.%2C%20Bienz-Tadmor%2CB.%2C%20Givol%2CD.%20and%20Oren%2CM.%0Atitle%3A%20Human%20p53%20cellular%20tumor%20antigen%3A%20cDNA%20sequence%20and%20expression%20in%20COS%20cells%0Ajournal%3A%20EMBO%20J.%204%20%285%29%2C%201251-1255%20%281985%29%0Amedline%20id%3A%20%0Apubmed%20id%3A%204006916%0Acomment%3A, [line 3]> location%3A%20%5B0%3A26144%5D%0Aauthors%3A%20Matlashewski%2CG.%2C%20Lamb%2CP.%2C%20Pim%2CD.%2C%20Peacock%2CJ.%2C%20Crawford%2CL.%20and%20Benchimol%2CS.%0Atitle%3A%20Isolation%20and%20characterization%20of%20a%20human%20p53%20cDNA%20clone%3A%20expression%20of%20the%20human%20p53%20gene%0Ajournal%3A%20EMBO%20J.%203%20%2813%29%2C%203257-3262%20%281984%29%0Amedline%20id%3A%20%0Apubmed%20id%3A%206396087%0Acomment%3A; [line 3]> accessions=NG_017013;data_file_division=PRI; [line 3]> date=19-FEB-2012;organism=Homo%20sapiens; [line 3]> gi=293651587 [line 4]> NG_017013.1 feature source 1 26144 . + .
[line 4]> db_xref=taxon%3A9606;mol_type=genomic%20DNA; [line 4]> organism=Homo%20sapiens;chromosome=17; [line 4]> map=17p13.1 [line 5]> NG_017013.1 feature gene 1 6475 . - .
[line 5]> note=WD%20repeat%20containing%2C%20antisense%20to%20TP53; [line 5]> db_xref=GeneID%3A55135,HGNC%3A25522, [line 5]> MIM%3A612661;gene=WRAP53;gene_synonym=DKCB3%3B%20TCAB1%3B%20WDR79 [line 6]> NG_017013.1 feature mRNA 2845 6475 . - .
[line 6]> db_xref=GI%3A221136857,GeneID%3A55135, [line 6]> HGNC%3A25522,MIM%3A612661;product=WD%20repeat%20containing%2C%20antisense%20to%20TP53%2C%20transcript%20variant%202; [line 6]> transcript_id=NM_001143990.1;inference=similar%20to%20RNA%20sequence%2C%20mRNA%20%28same%20species%29%3ARefSeq%3ANM_001143990.1; [line 6]> exception=annotated%20by%20transcript%20or%20proteomic%20data; [line 6]> gene=WRAP53;gene_synonym=DKCB3%3B%20TCAB1%3B%20WDR79; [line 6]> ID=NM_001143990.1 [line 7]> NG_017013.1 feature mRNA 2845 2956 . - .
[line 7]> Parent=NM_001143990.1 [line 8]> NG_017013.1 feature mRNA 3224 3322 . - .
[line 8]> Parent=NM_001143990.1 [line 9]> NG_017013.1 feature mRNA 3467 3898 . - .
[line 9]> Parent=NM_001143990.1 [line 10]> NG_017013.1 feature mRNA 6322 6475 . - .
[line 10]> Parent=NM_001143990.1

...

Line Number Error/Warning

---

4 [ERROR] invalid type (type: source) 7 [ERROR] invalid type pair - check all parents (at line 6; mRNA to mRNA) 12 [ERROR] invalid type pair - check all parents (at line 11; mRNA to mRNA) 17 [ERROR] invalid type pair - check all parents (at line 16; mRNA to mRNA) 22 [ERROR] invalid type pair - check all parents (at line 21; mRNA to mRNA) 26 [ERROR] invalid type pair - check all parents (at line 25; CDS to CDS) 30 [ERROR] invalid type pair - check all parents (at line 29; CDS to CDS) 34 [ERROR] invalid type pair - check all parents (at line 33; CDS to CDS) 38 [ERROR] invalid type pair - check all parents (at line 37; CDS to CDS) 44 [ERROR] invalid type pair - check all parents (at line 43; mRNA to mRNA) 56 [ERROR] invalid type pair - check all parents (at line 55; mRNA to mRNA) 69 [ERROR] invalid type pair - check all parents (at line 68; mRNA to mRNA) 82 [ERROR] invalid type pair - check all parents (at line 81; mRNA to mRNA) 94 [ERROR] invalid type pair - check all parents (at line 93; mRNA to mRNA) 113 [ERROR] invalid type pair - check all parents (at line 112; CDS to CDS) 124 [ERROR] invalid type pair - check all parents (at line 123; CDS to CDS) 135 [ERROR] invalid type pair - check all parents (at line 134; CDS to CDS) 145 [ERROR] invalid type pair - check all parents (at line 144; CDS to CDS) 162 [ERROR] invalid type pair - check all parents (at line 161; CDS to CDS) 171 [ERROR] invalid type pair - check all parents (at line 170; mRNA to mRNA) 180 [ERROR] invalid type pair - check all parents (at line 179; mRNA to mRNA) 189 [ERROR] invalid type pair - check all parents (at line 188; mRNA to mRNA) 206 [ERROR] invalid type pair - check all parents (at line 205; CDS to CDS) 214 [ERROR] invalid type pair - check all parents (at line 213; CDS to CDS) 221 [ERROR] invalid type pair - check all parents (at line 220; CDS to CDS)

 .''.      Hugo A. M. Torres : :' : . '   “Talk is cheap,  -    show me the code. ”  -- L. Torvalds.

On Mon, Mar 12, 2012 at 3:50 PM, A M Torres, Hugo mnemonico@posthocergopropterhoc.net wrote:

Thanks Brad. I will contact them and will let you know asap.

 .''.      Hugo A. M. Torres : :' : . '   “Talk is cheap,  -    show me the code. ”  -- L. Torvalds.

On Mon, Mar 12, 2012 at 3:04 PM, Brad Chapman reply@reply.github.com wrote:

Hugo; I think that the phase is correct but happy to adjust if the GenomeTools folks think otherwise. The GFF spec specifies the phase as 0,1 or 2:

http://www.sequenceontology.org/gff3.shtml

while codon_start from the GenBank file is 1, 2 or 3:

http://www.ddbj.nig.ac.jp/FT/full_index.html#7.2

so I've made the adjustment from 1 to 0 in the GFF output when converting. Let me know if your interaction with the GenomeTools developers indicate I've missed something in the conversion.

---

Reply to this email directly or view it on GitHub: https://github.com/chapmanb/bcbb/issues/52#issuecomment-4457847

[chapmanb]

Hugo; Thanks for this. The validator is complaining about 'source' not being present in the Sequence Ontology. Mapping GenBank to SO is a fairly large problem. I tried to tackle this a few years back but it ended up being too much work. Here's the progress I made:

http://bcbio.wordpress.com/2008/12/14/standard-ontologies-in-biosql/

Practically, most tools will not enforce this requirement, so being unable to map the entire thing I took the approach of keeping the output GFF similar to the input GenBank. If you wanted to take on a mapping of GenBank to Sequence Ontology I'd be happy to incorporate in.

Is GenomeTools requiring the ontology matches, or just that online validator?

[mercutio22]

Hi Brad,

Is GenomeTools requiring the ontology matches, or just that online validator?

---

Hmm, It seems only the validator. GenomeTools seems only to be complaining about that "phase" field.

I have already posted your considerations on their issue tracker. I will let you know what they say when I get a reply. In any case, thanks for taking the time you spent on looking at my problem.

[chapmanb]

Thanks Hugo -- let me know if there ends up being anything I can change on my end to improve the phase information. Hopefully that'll do it and get things working smoothly with GenomeTools. Thanks for your patience with this.

[chapmanb]

Hugo; I'm going to close this to clean up the issues. Hopefully everything was solved on the GenomeTools side. Thanks