[Biojava-l] Writing EMBL files

[Vasa Curcin]

Hello,

We are loading an EMBL file into a SequenceDB and then writing it out 
again and getting the following error:

16:42:19,032 INFO  [STDOUT]     at 
org.biojava.bio.seq.io.EmblFileFormer.addSequ
enceProperty(EmblFileFormer.java:246)
16:42:19,032 INFO  [STDOUT]     at 
org.biojava.bio.seq.io.SeqIOEventEmitter.getS
eqIOEvents(SeqIOEventEmitter.java:92)
16:42:19,032 INFO  [STDOUT]     at 
org.biojava.bio.seq.io.EmblLikeFormat.writeSe
quence(EmblLikeFormat.java:289)
16:42:19,032 INFO  [STDOUT]     at 
org.biojava.bio.seq.io.EmblLikeFormat.writeSe
quence(EmblLikeFormat.java:253)
16:42:19,032 INFO  [STDOUT]     at 
org.biojava.bio.seq.io.StreamWriter.writeStre
am(StreamWriter.java:63)
16:42:19,032 INFO  [STDOUT]     at 
org.biojava.bio.seq.io.SeqIOTools.writeEmbl(S
eqIOTools.java:289)
16:42:19,032 INFO  [STDOUT]     at 
SequenceDBToText.process(SequenceDBToText.jav
a:134)

This is the file we are using:

ID   AB126240   standard; genomic DNA; PRO; 1350 BP.
XX
AC   AB126240;
XX
SV   AB126240.1
XX
DT   03-SEP-2004 (Rel. 81, Created)
DT   03-SEP-2004 (Rel. 81, Last updated, Version 1)
XX
DE   Thermococcus kodakaraensis Tko1062 gene for phosphosugar mutase, 
complete
DE   cds.
XX
KW   .
XX
OS   Thermococcus kodakaraensis
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Thermococcus.
XX
RN   [1]
RP   1-1350
RA   Imanaka T., Atomi H., Rashid N.;
RT   ;
RL   Submitted (15-NOV-2003) to the EMBL/GenBank/DDBJ databases.
RL   Tadayuki Imanaka, Kyoto University, Synthetic Chemistry & Biological
RL   Chemistry, Graduate School of Engineering; Katsura, Nishikyo-ku, Kyoto
RL   615-8510, Japan (E-mail:imanaka at sbchem.kyoto-u.ac.jp, 
Tel:81-75-383-2777,
RL   Fax:81-75-383-2778)
XX
RN   [2]
RA   Rashid N., Kanai T., Atomi H., Imanaka T.;
RT   "Among Multiple Phosphomannomutase Gene Orthologues, Only One Gene 
Encodes
RT   a Protein with Phosphoglucomutase and Phosphomannomutase Activities in
RT   Thermococcus kodakaraensis";
RL   J. Bacteriol. 186:6070-6076(2004).
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..1350
FT                   /db_xref="taxon:69014"
FT                   /mol_type="genomic DNA"
FT                   /organism="Thermococcus kodakaraensis"
FT                   /strain="KOD1"
FT   CDS             1..1350
FT                   /codon_start=1
FT                   /transl_table=11
FT                   /gene="Tko1062"
FT                   /product="phosphosugar mutase"
FT                   /protein_id="BAD42439.1"
FT                   
/translation="MGKYFGTSGIREVFNEKLTPELALKVGKALGTYLGGGKVVIGKDT
FT                   
RTSGDVIKSAVISGLLSTGVDVIDIGLAPTPLTGFAIKLYGADAGVTITASHNPPEYNG
FT                   
IKVWQANGMAYTSEMERELESIMDSGNFKKAPWNEIGTLRRADPSEEYINAALKFVKLE
FT                   
NSYTVVLDSGNGAGSVVSPYLQRELGNRVISLNSHPSGFFVRELEPNAKSLSALAKTVR
FT                   
VMKADVGIAHDGDADRIGVVDDQGNFVEYEVMLSLIAGYMLRKFGKGKIVTTVDAGFAL
FT                   
DDYLRPLGGEVIRTRVGDVAVADELAKHGGVFGGEPSGTWIIPQWNLTPDGIFAGALVL
FT                   
EMIDRLGPISELAKEVPRYVTLRAKIPCPNEKKAKAMEIIAREALKTFDYEGLIDIDGI
FT                   RIENGDWWILFRPSGTEPIMRITLEAHEEEKAKELMGKAERLVKKAISEA"
XX
SQ   Sequence 1350 BP; 339 A; 341 C; 417 G; 253 T; 0 other;
     atggggaagt acttcggaac cagcggaatc agggaagtct ttaatgagaa 
gctgacacct        60
     gagctggctc taaaggtcgg caaagccctt ggaacgtacc tcggcggcgg 
aaaggttgtt       120
     atcgggaagg ataccaggac tagcggcgac gttataaaat cagcagtcat 
aagcggactt       180
     ctctcaactg gtgttgatgt gattgacata ggtttagcgc caacgccgct 
cacgggcttt       240
     gcgataaagc tctacggtgc cgatgctggc gttaccatca cagcttctca 
caacccgccg       300
     gagtacaacg gcataaaggt gtggcaggcc aacggaatgg catacacctc 
tgagatggag       360
     cgtgaactcg agtccataat ggactcaggg aacttcaaaa aagctccctg 
gaatgagatc       420
     gggacgctta gaagggccga ccccagtgag gagtacataa acgcggcgct 
aaaattcgtc       480
     aaacttgaga actcctacac ggtcgtcctc gattctggaa acggtgcggg 
ctcggtggtc       540
     tccccctacc tccagcggga gctgggcaat agggttatct cgctcaactc 
ccacccgagc       600
     ggcttcttcg tcagggaact tgagccgaac gcgaagagcc tctccgccct 
agcgaagacc       660
     gttagagtga tgaaagccga cgtcggcata gcccacgacg gcgacgcaga 
taggatcggc       720
     gtcgttgatg atcagggcaa cttcgttgag tacgaggtca tgctctcgct 
catagcgggc       780
     tacatgctga ggaagttcgg gaaggggaaa atagttacca ccgttgatgc 
gggctttgct       840
     ttggacgact acctcagacc ccttggcgga gaagtcataa ggacgcgcgt 
tggtgatgtg       900
     gccgttgccg acgagctcgc aaaacacggc ggcgtcttcg gcggcgagcc 
gagtggcacg       960
     tggataatcc cgcagtggaa cctcaccccc gacggaatct ttgctggggc 
ccttgttctg      1020
     gagatgattg acagactcgg tccgataagc gagctggcca aggaagtccc 
gcgctacgtg      1080
     acgctccgcg ccaaaatccc ctgtccgaac gagaagaagg cgaaagccat 
ggagataata      1140
     gcgcgcgagg cactaaagac gttcgactac gaggggctga tagacataga 
tggaattagg      1200
     atagaaaacg gtgactggtg gatcctcttc cgcccgagcg gaaccgagcc 
gataatgcgc      1260
     ataactttgg aggcccacga ggaagagaag gcgaaggagc tgatggggaa 
ggcggagagg      1320
     ctggttaaga aagccatctc 
ggaggcctga                                       1350
//

 
Any ideas?

Regards,
Vasa