[Biojava-l] Parsing Genbank/EMBL/XML Sequences from binary NCBI ASN.1 daily update files

[Seth Johnson]

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  JOURNAL   Unpublished (2005)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
>
>