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 --------------- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
