[Biojava-l] [biojavax] EMBL parser error
Richard Holland
richard.holland at ebi.ac.uk
Fri Apr 7 13:42:10 UTC 2006
Hi. Someone else had checked in a change to a different class, but that
change was incorrect and didn't compile. It should compile now.
cheers,
Richard
PS. Note to all those who commit changes - PLEASE check your code
compiles first before committing it!
On Fri, 2006-04-07 at 15:07 +0200, Morgane THOMAS-CHOLLIER wrote:
> I tried to checkout biojava-live but it seems I cannot build it anymore.
> I get the following error :
>
> compile-biojava:
> [javac] Compiling 1321 source files to
> /Users/morgane/Documents/PHD/KermitDB/Kermit_workspace/biojava-live3/ant-build/classes/biojava
> [javac]
> /Users/morgane/Documents/PHD/KermitDB/Kermit_workspace/biojava-live3/src/org/biojavax/utils/StringTools.java:97:
> exception java.io.IOException is never thrown in body of corresponding
> try statement
> [javac] } catch (IOException e) {
> [javac] ^
> [javac] Note: Some input files use or override a deprecated API.
> [javac] Note: Recompile with -deprecation for details.
> [javac] 1 error
>
> I use Mac OS X 10.3.9, java 1.4.2.
>
> Hope you could help,
>
> Cheers,
>
> Morgane.
>
>
> Richard Holland wrote:
>
> >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
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