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 and example sequence files below. The line from 1141 to 1200
disappears.
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));
}
}
___________________________________________
SEQUENCE IN:
AC ENSG00000105974;
FT exon 1100..1199
FT /end_phase="2"
FT /exon_id="ENSE00001085899"
FT /start_phase="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
//
SEQUENCE OUT:
AC ENSG00000105974;
FT exon 1100..1199
FT /end_phase="2"
FT /exon_id="ENSE00001085899"
FT /start_phase="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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