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Writing EMBL files: msg#00037java.bio.general
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 _______________________________________________ Biojava-l mailing list - Biojava-l@xxxxxxxxxxx http://biojava.org/mailman/listinfo/biojava-l
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