[Biojava-l] writesequence problem

[Stein Aerts]

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Hello,
There appears to be a problem when writing a sequence to file in EMBL
format, but only if it contains a multiple of 60 nucleotides (there are 60
nt's on each line): the last line of nucleotides is not written and the
nucleotide-count of the last line is incorrect.

Example code below and example sequence files in attachment.

Best regards,
Stein Aerts.

________________________________________

import org.biojava.bio.seq.io.*;
import org.biojava.bio.seq.*;
import java.io.*;

public class TestEmbl {


  public static void main(String[] args) throws Exception {
    Sequence seq = null;
    BufferedReader br = new BufferedReader(new
FileReader("D:\\SAE\\temp\\test_in.embl"));
    SequenceIterator stream = SeqIOTools.readEmbl(br);
    if (stream.hasNext()){
      seq = stream.nextSequence();
    }
    SequenceFormat format = new EmblLikeFormat();
    OutputStream out = new FileOutputStream("D:\\SAE\\temp\\test_out.embl");
    format.writeSequence(seq, new PrintStream(out));
  }
}

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	name="test_out.embl"
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	filename="test_out.embl"

AC   ENSG00000105974;
FT   exon            1100..1199
FT                   /end_phase=3D"2"
FT                   /exon_id=3D"ENSE00001085899"
FT                   /start_phase=3D"0"
XX
SQ   Sequence 1200 BP; 328 A; 282 C; 232 G; 358 T; 0 other;
     tcctttatag ttcttttata cttttgtgtc ttctctctaa ctaaataatc aactctttca   =
     60
     gcattccatc catttccctt tctcctccct cttactccca acccacattc ccctctccat   =
    120
     tttaatttta acctgtgccc cttcaagtgt actccagctt tttttttaaa ataatttcaa   =
    180
     gtgatacttt gacttttgac tgcatatgga agcataagta acatgtcctt tcatttttgg   =
    240
     ataatgagtt tcctgattaa ttacagctca agagtaaaat gactgattac tatttaattc   =
    300
     attttgtgct tctttacaat aaagtaaaga cagaagcccc agattcagga acagacaaaa   =
    360
     tactttaatc gctatcacat tttttttaag tctagtcaat tagaaaagtc aaatctttcc   =
    420
     tcacagccaa gcacattaaa aaaaaatctt ctctggtaat aaacttgaag ctttaaataa   =
    480
     ttctacaatt ataaacattt tgtgtatttt gcaaatatgg cataacctgt tggcataaaa   =
    540
     ttccattgtt ccagaaaata tcggtaataa aattatagaa aagttaaaga tcttcatttc   =
    600
     ttatttcgaa gcgtttggga gacatttcag aaacggatgg gaaatgttaa attctgcatg   =
    660
     cctgcttaag tttccatcca caccgactag atgtaaacga gtgtcaccaa aagtacacca   =
    720
     caggcaccca cacagattcc ttccataagg gatccacaaa gtttagatgt gaaatgtacc   =
    780
     taaaggttcc tagccgtctt tcatccctcc ctctgtgaaa cagggagaca catgtgtttt   =
    840
     aaggcagaga tggaacttgg gcgatgggcg gggggtgggg gaggtgggaa gggacggctt   =
    900
     aggacagggc aggattgtgg attgtttctg ccgccttggt tgcccatact gggcatctct   =
    960
     gcaggcgcgt cggctccctc cacccctgct gagatgatgc actgcgaaaa cattcgctct   =
   1020
     ccccgggacg cctctcggtg gttcagagca gggaaaatgt tgcctcaggt ttaaaataat   =
   1080
     ctgcccaagc accccagcgc gggagaaacg ttctcactcg ctctctgctc gctgcgggcg   =
   1140
                                                                         =
   1140
//

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	name="test_in.embl"
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	filename="test_in.embl"

AC   ENSG00000105974;
FT   exon            1100..1199
FT                   /end_phase=3D"2"
FT                   /exon_id=3D"ENSE00001085899"
FT                   /start_phase=3D"0"
XX
SQ   Sequence 1200 BP; 328 A; 283 C; 231 G; 358 T; 0 other;
     tcctttatag ttcttttata cttttgtgtc ttctctctaa ctaaataatc aactctttca   =
     60
     gcattccatc catttccctt tctcctccct cttactccca acccacattc ccctctccat   =
    120
     tttaatttta acctgtgccc cttcaagtgt actccagctt tttttttaaa ataatttcaa   =
    180
     gtgatacttt gacttttgac tgcatatgga agcataagta acatgtcctt tcatttttgg   =
    240
     ataatgagtt tcctgattaa ttacagctca agagtaaaat gactgattac tatttaattc   =
    300
     attttgtgct tctttacaat aaagtaaaga cagaagcccc agattcagga acagacaaaa   =
    360
     tactttaatc gctatcacat tttttttaag tctagtcaat tagaaaagtc aaatctttcc   =
    420
     tcacagccaa gcacattaaa aaaaaatctt ctctggtaat aaacttgaag ctttaaataa   =
    480
     ttctacaatt ataaacattt tgtgtatttt gcaaatatgg cataacctgt tggcataaaa   =
    540
     ttccattgtt ccagaaaata tcggtaataa aattatagaa aagttaaaga tcttcatttc   =
    600
     ttatttcgaa gcgtttggga gacatttcag aaacggatgg gaaatgttaa attctgcatg   =
    660
     cctgcttaag tttccatcca caccgactag atgtaaacga gtgtcaccaa aagtacacca   =
    720
     caggcaccca cacagattcc ttccataagg gatccacaaa gtttagatgt gaaatgtacc   =
    780
     taaaggttcc tagccgtctt tcatccctcc ctctgtgaaa cagggagaca catgtgtttt   =
    840
     aaggcagaga tggaacttgg gcgatgggcg gggggtgggg gaggtgggaa gggacggctt   =
    900
     aggacagggc aggattgtgg attgtttctg ccgccttggt tgcccatact gggcatctct   =
    960
     gcaggcgcgt cggctccctc cacccctgct gagatgatgc actgcgaaaa cattcgctct   =
   1020
     ccccgggacg cctctcggtg gttcagagca gggaaaatgt tgcctcaggt ttaaaataat   =
   1080
     ctgcccaagc accccagcgc gggagaaacg ttctcactcg ctctctgctc gctgcgggcg   =
   1140
     ctgcccaagc accccagcgc gggagaaacg ttctcactcg ctctctgctc gctgcgggcg   =
   1200
//
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