[Biojava-l] [biojavax] EMBL parser error

[Richard Holland]

Sorry, my bad. An off-by-one error... 

Check it out again and see if it works now.

cheers,
Richard

PS. I don't have any EMBL files to test with at the moment otherwise I'd
check it myself... :)


On Fri, 2006-04-07 at 14:18 +0200, Morgane THOMAS-CHOLLIER wrote:
> I now get another error message with the same file :
> 
> Exception in thread "main" org.biojava.bio.BioException: Could not read 
> sequence
>     at 
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111)
>     at 
> org.embnet.be.biojavax.tryout.EMBLParseTest.main(EMBLParseTest.java:34)
> Caused by: java.lang.IndexOutOfBoundsException: No group 5
>     at java.util.regex.Matcher.group(Matcher.java:355)
>     at 
> org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:271)
>     at 
> org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108)
>     ... 1 more
> 
> Here is the complete file, for info:
> 
> ID   DQ158013   standard; genomic DNA; VRT; 118 BP.
> XX
> AC   DQ158013;
> XX
> SV   DQ158013.1
> XX
> DT   19-JAN-2006 (Rel. 86, Created)
> DT   19-JAN-2006 (Rel. 86, Last updated, Version 1)
> XX
> DE   Triturus helveticus clone Thel.b9 HOXB9 (Hoxb9) gene, partial cds.
> XX
> KW   .
> XX
> OS   Triturus helveticus (palmate newt)
> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; 
> Amphibia;
> OC   Batrachia; Caudata; Salamandroidea; Salamandridae; Triturus.
> XX
> RN   [1]
> RP   1-118
> RX   DOI; 10.1016/j.ympev.2005.08.012.
> RX   PUBMED; 16198128.
> RA   Mannaert A., Roelants K., Bossuyt F., Leyns L.;
> RT   "A PCR survey for posterior Hox genes in amphibians";
> RL   Mol. Phylogenet. Evol. 38(2):449-458(2006).
> XX
> RN   [2]
> RP   1-118
> RA   Mannaert A., Roelants K., Bossuyt F., Leyns L.;
> RT   ;
> RL   Submitted (09-AUG-2005) to the EMBL/GenBank/DDBJ databases.
> RL   Biology Department, Vrije Universiteit Brussel, Pleinlaan 2, 
> Brussels 1050,
> RL   Belgium
> XX
> FH   Key             Location/Qualifiers
> FH
> FT   source          1..118
> FT                   /organism="Triturus helveticus"
> FT                   /mol_type="genomic DNA"
> FT                   /clone="Thel.b9"
> FT                   /db_xref="taxon:256425"
> FT   gene            <1..>118
> FT                   /gene="Hoxb9"
> FT                   /note="Hoxb-9"
> FT   mRNA            <1..>118
> FT                   /gene="Hoxb9"
> FT                   /product="HOXB9"
> FT   CDS             <1..>118
> FT                   /codon_start=2
> FT                   /gene="Hoxb9"
> FT                   /product="HOXB9"
> FT                   /db_xref="UniProtKB/TrEMBL:Q2LK47"
> FT                   /protein_id="ABA39736.1"
> FT                   /translation="KYQTLELEKEFLFNMYLTRDRRHEVARLLNLSERQVKIW"
> XX
> SQ   Sequence 118 BP; 28 A; 35 C; 37 G; 18 T; 0 other;
>      caaataccag acgctggagc tggagaagga gttcctgttc aacatgtacc 
> tcacccggga        60
>      ccgcaggcac gaggtggccc ggctgctgaa cctcagcgag cgccaggtca 
> agatctgg         118
> //
> 
> Thanks for helping,
> 
> Morgane.
> 
> Richard Holland wrote:
> 
> >That was indeed a bug. I have made a change to the date parsing in
> >EMBLFormat and committed it to CVS. Could you test it for me please?
> >
> >cheers,
> >Richard
> >
> >On Fri, 2006-04-07 at 11:20 +0200, Morgane THOMAS-CHOLLIER wrote:
> >  
> >
> >>Hello,
> >>
> >>I am currently using biojavax that I checked out today from CVS to parse 
> >>an EMBL file, exported from EBI SRS server.
> >>
> >>I ran into this error :
> >>
> >>Exception in thread "main" org.biojava.bio.BioException: Could not read 
> >>sequence
> >>    at 
> >>org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:111)
> >>    at 
> >>org.embnet.be.biojavax.tryout.EMBLParseTest.main(EMBLParseTest.java:34)
> >>Caused by: org.biojava.bio.seq.io.ParseException: Bad date type found: 86
> >>    at 
> >>org.biojavax.bio.seq.io.EMBLFormat.readRichSequence(EMBLFormat.java:278)
> >>    at 
> >>org.biojavax.bio.seq.io.RichStreamReader.nextRichSequence(RichStreamReader.java:108)
> >>    ... 1 more
> >>
> >>The EMBL file is :
> >>
> >>ID   DQ158013   standard; genomic DNA; VRT; 118 BP.
> >>XX
> >>AC   DQ158013;
> >>XX
> >>SV   DQ158013.1
> >>XX
> >>DT   19-JAN-2006 (Rel. 86, Created)
> >>DT   19-JAN-2006 (Rel. 86, Last updated, Version 1)
> >>XX
> >>DE   Triturus helveticus clone Thel.b9 HOXB9 (Hoxb9) gene, partial cds.
> >>
> >>Removing the two lines that comprise the date information resolves the 
> >>problem.
> >>
> >>Thanks,
> >>
> >>Morgane.
> >>
> >>    
> >>
> 
> -- 
> **********************************************************
> Morgane THOMAS-CHOLLIER, PHD Student
> 
> Vrije Universiteit Brussels (VUB)
> Laboratory of Cell Genetics
> Pleinlaan 2
> 1050 Brussels
> Belgium
> 
-- 
Richard Holland
European Bioinformatics Institute
Wellcome Trust Genome Campus, Hinxton
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-494416
---------------