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Writing EMBL files: msg#00037

java.bio.general

Subject: Writing EMBL files

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@xxxxxxxxxxxxxxxxxxxx, 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
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