[Biojava-l] Parsing Genbank/EMBL/XML Sequences from binary NCBI ASN.1 daily update files
Seth Johnson
johnson.biotech at gmail.com
Mon Jun 5 16:28:30 UTC 2006
I agree with you on that one. However, the problem might be a little
deeper. Same '?' appear in the INSDseq format bounded by
<INSDReference_reference> tags and cause the following exception.
This tells me that the '?' are actually values that are being
incorrectly parsed. Further examination of the .dtd reveals that
INSDseqFormat.java is tailord towards the INSDSeq v. 1.3 whereas the
files I obtain are in the INSDSeq v. 1.4 (which among other things
contain a new tag <INSDReference_position>). Here're links to both
.dtd's:
http://www.ebi.ac.uk/embl/Documentation/DTD/INSDSeq_v1.3.dtd.txt
http://www.ebi.ac.uk/embl/Documentation/DTD/INSDC_V1.4.dtd.txt
I think it might be worth accommodating changes for the INSDseq
format, not sure how that would affect the '?' in Genbank.
Seth
======================
org.biojava.bio.BioException: Could not read sequence
at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
at exonhit.parsers.GenBankParser.main(GenBankParser.java:348)
Caused by: org.biojava.bio.seq.io.ParseException:
org.biojava.bio.seq.io.ParseException: Bad reference line found: ?
at org.biojavax.bio.seq.io.INSDseqFormat.readRichSequence(INSDseqFormat.java:250)
at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
... 1 more
Caused by: org.biojava.bio.seq.io.ParseException: Bad reference line found: ?
at org.biojavax.bio.seq.io.INSDseqFormat$INSDseqHandler.endElement(INSDseqFormat.java:901)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.endElement(AbstractSAXParser.java:633)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanEndElement(XMLDocumentFragmentScannerImpl.java:1241)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(XMLDocumentFragmentScannerImpl.java:1685)
at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:368)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:834)
at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:764)
at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:148)
at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1242)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:375)
at org.biojavax.utils.XMLTools.readXMLChunk(XMLTools.java:97)
at org.biojavax.bio.seq.io.INSDseqFormat.readRichSequence(INSDseqFormat.java:246)
... 2 more
Java Result: -1
======================
~~~~~~~~~~~~~~~~~~~~~~
<INSDSeq_references>
<INSDReference>
<INSDReference_reference>?</INSDReference_reference>
<INSDReference_position>1..16732</INSDReference_position>
<INSDReference_authors>
<INSDAuthor>Bjornerfeldt,S.</INSDAuthor>
<INSDAuthor>Webster,M.T.</INSDAuthor>
<INSDAuthor>Vila,C.</INSDAuthor>
</INSDReference_authors>
<INSDReference_title>Relaxation of Selective Constraint on Dog
Mitochondrial DNA Following Domestication</INSDReference_title>
<INSDReference_journal>Unpublished</INSDReference_journal>
</INSDReference>
<INSDReference>
<INSDReference_reference>?</INSDReference_reference>
<INSDReference_position>1..16732</INSDReference_position>
<INSDReference_authors>
<INSDAuthor>Bjornerfeldt,S.</INSDAuthor>
<INSDAuthor>Webster,M.T.</INSDAuthor>
<INSDAuthor>Vila,C.</INSDAuthor>
</INSDReference_authors>
<INSDReference_journal>Submitted (06-APR-2006) to the
EMBL/GenBank/DDBJ databases. Evolutionary Biology, Evolutionary
Biology, Norbyvagen 18D, Uppsala 752 36,
Sweden</INSDReference_journal>
</INSDReference>
</INSDSeq_references>
~~~~~~~~~~~~~~~~~~~~~~
On 6/5/06, Richard Holland <richard.holland at ebi.ac.uk> wrote:
> Hmmm... interesting. I _could_ put in a special case that ignores the
> question marks, but that wouldn't be 'nice' really - this is more of a
> problem with the program that is producing the Genbank files than a
> problem with the parser trying to read them. '?' is not a valid tag in
> the official Genbank format, and has no meaning attached to it that I
> can work out, so I'm reluctant to make the parser recognise it.
>
> I'd suggest you contact the people who write the software you are using
> to produce the Genbank files and ask them if they could stick to the
> rules!
>
> In the meantime you could work around the problem by stripping the
> question marks in some kind of pre-processor before passing it onto
> BioJavaX for parsing.
>
> cheers,
> Richard
>
> On Mon, 2006-06-05 at 11:39 -0400, Seth Johnson wrote:
> > Removing '?' (or several of them in my case) avoids the following exception:
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > org.biojava.bio.BioException: Could not read sequence
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
> > at exonhit.parsers.GenBankParser.main(GenBankParser.java:348)
> > Caused by: org.biojava.bio.seq.io.ParseException: DQ415957
> > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:245)
> > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
> > ... 1 more
> > Java Result: -1
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > I don't know where that previous tokenization problem came from since
> > I can no longer reproduce it. This time it's more or less straight
> > forward.
> > Here's the original file with question marks:
> > ============================
> > LOCUS DQ415957 1437 bp mRNA linear VRT 01-JUN-2006
> > DEFINITION Danio rerio capillary morphogenesis protein 2A (cmg2a) mRNA,
> > complete cds.
> > ACCESSION DQ415957
> > VERSION DQ415957.1 GI:89513612
> > KEYWORDS .
> > SOURCE Unknown.
> > ORGANISM Unknown.
> > Unclassified.
> > ?
> > ?
> > FEATURES Location/Qualifiers
> > ?
> > gene 1..1437
> > /gene="cmg2a"
> > CDS 1..1437
> > /gene="cmg2a"
> > /note="cell surface receptor; similar to anthrax toxin
> > receptor 2 (ANTXR2, ATR2, CMG2)"
> > /codon_start=1
> > /product="capillary morphogenesis protein 2A"
> > /protein_id="ABD74633.1"
> > /db_xref="GI:89513613"
> > /translation="MTKENLWSVATTATLFFCLCFSSFKAETPSCHGAYDLYFVLDRS
> > GSVSTDWSEIYDFVKNLTERFVSPNLRVSFIVFSSRAEIVLPLTGDRSEINKGLKTLS
> > EVNPAGETYMHEGIKLATEQMKKEPKKSSSIIVALTDGKLETYIHQLTIDEADSARKY
> > GARVYCVGVKDFDEEQLADVADSKEQVFPVKGGFQALKGIVNSILKQSCTEILTVEPS
> > SVCVNQSFDIVLRGNGFAVGRQTEGVICSFIVDGVTYKQKPTKVKIDYILCPAPVLYT
> > VGQQMEVLISLNSGTSYITSAFIITASSCSDGTVVAIVFLVLFLLLALALMWWFWPLC
> > CTVVIKDPPPQRPPPPPPKLEPDPEPKKKWPTVDASYYGGRGAGGIKRMEVRWGEKGS
> > TEEGARLEMAKNAVVSIQEESEEPMVKKPRAPAQTCHQSESKWYTPIRGRLDALWALL
> > RRQYDRVSVMRPTSADKGRCMNFSRTQH"
> > ORIGIN
> > 1 atgacaaagg aaaatctctg gagcgtggca accacggcga ctcttttctt ctgtttatgc
> > 61 ttttcatctt ttaaagcgga aaccccatct tgtcatggtg cctacgacct gtactttgtg
> > 121 ttggaccgat ctggaagtgt ttcgactgac tggagtgaaa tctatgactt tgtcaaaaat
> > 181 cttacagaga gatttgtgag tccaaatctg cgagtgtcct tcattgtttt ttcatcaaga
> > 241 gcagagattg tgttaccgct cactggagac aggtcagaaa ttaataaagg cctgaagacc
> > 301 ttaagtgagg tcaatccagc tggagaaaca tacatgcatg aaggaattaa attggcaact
> > 361 gaacaaatga aaaaagagcc taaaaagtcc tctagtatta ttgtggcctt gactgatgga
> > 421 aagcttgaaa cgtatatcca tcaactcact attgacgagg ctgattcagc aaggaagtat
> > 481 ggggctcgtg tgtactgtgt tggtgtaaaa gactttgatg aagaacagct agccgatgtg
> > 541 gctgattcca aggagcaagt gttcccagtc aaaggaggct ttcaggctct caaaggcatc
> > 601 gttaactcga tcctcaagca atcatgcacc gaaatcctaa cagtggaacc gtccagcgtc
> > 661 tgcgtgaacc agtcctttga cattgttttg agagggaacg ggttcgcagt ggggagacaa
> > 721 acagaaggag tcatctgcag tttcatagtg gatggagtta cttacaaaca aaaaccaacc
> > 781 aaagtgaaga ttgactacat cctatgtcct gctccagtgc tgtatacagt tggacagcaa
> > 841 atggaggttc tgatcagttt gaacagtgga acatcatata tcaccagtgc tttcatcatc
> > 901 actgcctctt catgttcgga cggcacagtg gtggccattg tgttcttggt gctttttctc
> > 961 ctgttggctt tggctctgat gtggtggttc tggcctctat gctgcactgt cgttattaaa
> > 1021 gacccacctc cacaaagacc tcctccacct ccacctaagc tagagccaga cccggaaccc
> > 1081 aagaagaagt ggccaactgt ggatgcatct tactatgggg gaagaggagc tggtggaatc
> > 1141 aaacgcatgg aggtccgttg gggagaaaaa gggtctacag aggaaggtgc aagactagag
> > 1201 atggctaaga atgcagtagt gtcaatacaa gaggaatcag aagaacccat ggtcaaaaag
> > 1261 ccaagagcac ctgcacaaac atgccatcaa tctgaatcca agtggtatac accaatcaga
> > 1321 ggccgtcttg acgcactgtg ggctcttttg cggcggcaat atgaccgagt ttcagttatg
> > 1381 cgaccaactt ctgcagataa gggtcgctgt atgaatttca gtcgcacgca gcattaa
> > //
> >
> > ============================
> >
> >
> > On 6/5/06, Richard Holland <richard.holland at ebi.ac.uk> wrote:
> > > Hi again.
> > >
> > > Could you remove the offending question mark from the GenBank file and
> > > try it again to see if that fixes it? The parser should just ignore it
> > > but apparently not. The error looks weird to me because the tokenization
> > > for a DNA GenBank file _does_ contain the letter 't'! Not sure what's
> > > going on here.
> > ...
> > >
> > > cheers,
> > > Richard
> > >
> > > On Mon, 2006-06-05 at 10:37 -0400, Seth Johnson wrote:
> > > > Hell again Richard,
> > > >
> > > > No sooner I've said about the fix of the last parsing exception than
> > > > another one came up with Genbank format:
> > > > --------------------------------------
> > > > org.biojava.bio.seq.io.ParseException: DQ431065
> > > > org.biojava.bio.BioException: Could not read sequence
> > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:112)
> > > > at exonhit.parsers.GenBankParser.getGBSequences(GenBankParser.java:151)
> > > > at exonhit.parsers.GenBankParser.runGBparser(GenBankParser.java:246)
> > > > at exonhit.parsers.GenBankParser.main(GenBankParser.java:326)
> > > > Caused by: org.biojava.bio.seq.io.ParseException: DQ431065
> > > > at org.biojavax.bio.seq.io.GenbankFormat.readRichSequence(GenbankFormat.java:245)
> > > > at org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:109)
> > > > ... 3 more
> > > > org.biojava.bio.seq.io.ParseException:
> > > > org.biojava.bio.symbol.IllegalSymbolException: This tokenization
> > > > doesn't contain character: 't'
> > > > ----------------------------------------
> > > > The Genbank file that caused it is as follows:
> > > > =========================================
> > > > LOCUS DQ431065 425 bp DNA linear INV 01-JUN-2006
> > > > DEFINITION Reticulitermes sp. ALS-2006c 16S ribosomal RNA gene, partial
> > > > sequence; mitochondrial.
> > > > ACCESSION DQ431065
> > > > VERSION DQ431065.1 GI:90102206
> > > > KEYWORDS .
> > > > SOURCE Vaccinium corymbosum
> > > > ORGANISM Vaccinium corymbosum
> > > > Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
> > > > Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons;
> > > > asterids; Ericales; Ericaceae; Vaccinioideae; Vaccinieae;
> > > > Vaccinium.
> > > > ?
> > > > REFERENCE 2 (bases 1 to 425)
> > > > AUTHORS Naik,L.D. and Rowland,L.J.
> > > > TITLE Expressed Sequence Tags of cDNA clones from subtracted library of
> > > > Vaccinium corymbosum
> > > > JOURNAL Unpublished (2005)
> > > > FEATURES Location/Qualifiers
> > > > source 1..425
> > > > /organism="Vaccinium corymbosum"
> > > > /mol_type="genomic DNA"
> > > > /cultivar="Bluecrop"
> > > > /db_xref="taxon:69266"
> > > > /tissue_type="Flower buds"
> > > > /clone_lib="Subtracted cDNA library of Vaccinium
> > > > corymbosum"
> > > > /dev_stage="399 hour chill unit exposure"
> > > > /note="Vector: pCR4TOPO; Site_1: Eco R I; Site_2: Eco R I"
> > > > rRNA <1..>425
> > > > /product="16S ribosomal RNA"
> > > > ORIGIN
> > > > 1 cgcctgttta tcaaaaacat cttttcttgt tagtttttga agtatggcct gcccgctgac
> > > > 61 tttagtgttg aagggccgcg gtattttgac cgtgcaaagg tagcatagtc attagttctt
> > > > 121 taattgtgat ctggtatgaa tggcttgacg aggcatgggc tgtcttaatt ttgaattgtt
> > > > 181 tattgaattt ggtctttgag ttaaaattct tagatgtttt tatgggacga gaagacccta
> > > > 241 tagagtttaa catttattat ggtccttttc tgtttgtgag ggctcactgg gccgtctaat
> > > > 301 atgttttgtt ggggtgatgg gagggaataa tttaacccct cctttttatt attatattta
> > > > 361 tttatattta tttgatccat ttattttgat tgtaagatta aattacctta gggataacag
> > > > 421 cgtaa
> > > > //
> > > > ==================================
> > > > I think it's the presence of the '?' at the beginning of the line?!?!
> > > > I'm not sure wether the information that was supposed to be present
> > > > instead of those question marks is absent from the original ASN.1
> > > > batch file or it's a bug in the NCBI ASN2GO software. It looks to me
> > > > that the former is the case since the file from NCBI website contains
> > > > much more information than the batch file. Just bringing this to
> > > > everyone's attention.
> > > >
> > > >
> > > > --
> > > > Best Regards,
> > > >
> > > >
> > > > Seth Johnson
> > > > Senior Bioinformatics Associate
> > > >
> > > > Ph: (202) 470-0900
> > > > Fx: (775) 251-0358
> > > >
> > > > On 6/2/06, Richard Holland <richard.holland at ebi.ac.uk> wrote:
> > > > > Hi Seth.
> > > > >
> > > > > Your second point, about the authors string not being read correctly in
> > > > > Genbank format, has been fixed (or should have been if I got the code
> > > > > right!). Could you check the latest version of biojava-live out of CVS
> > > > > and give it another go? Basically the parser did not recognise the
> > > > > CONSRTM tag, as it is not mentioned in the sample record provided by
> > > > > NCBI, which is what I based the parser on.
> > > > ...
> > > > >
> > > > > cheers,
> > > > > Richard
> > > > >
> > > > >
> > > --
> > > Richard Holland (BioMart Team)
> > > EMBL-EBI
> > > Wellcome Trust Genome Campus
> > > Hinxton
> > > Cambridge CB10 1SD
> > > UNITED KINGDOM
> > > Tel: +44-(0)1223-494416
> > >
> > >
> >
> >
> --
> Richard Holland (BioMart Team)
> EMBL-EBI
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> UNITED KINGDOM
> Tel: +44-(0)1223-494416
>
>
--
Best Regards,
Seth Johnson
Senior Bioinformatics Associate
Ph: (202) 470-0900
Fx: (775) 251-0358
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