[Biojava-l] Writing Genbank Files

[David Waring]

Is the GenbankFormat supposed to write full genbank files? If I read a
genbank file and then write it I just get the Accession tag the features
(but no Feature tag) and the sequence. Looking at the GenbankFileFormer,
it looks like this is all it can handle. What's up?


CODE snippet
        SequenceIterator sI = SeqIOTools.readGenbank(gbbr);
        Sequence seq = sI.nextSequence();
        PrintStream ps = new PrintStream(os);
        sf = new GenbankFormat();
        sf.writeSequence(seq,ps);


Output file looks like

ACCESSION   AL138845
     source          1..121558
                     /chromosome="1"
                     /clone="RP4-781A20"
                     /clone_lib="RPCI-4"
                     /db_xref="taxon:9606"
                     /map="p32.1-32.3"
                     /organism="Homo sapiens"
     misc_feature    1..4804

/note="assembly_fragment:00708fragment_chain:1clone_end:SP6
                     vector_side:left"
     misc_feature    4905..16118
                     /note="assembly_fragment:00650fragment_chain:1"


..... then the sequence




Input file looked like .....

LOCUS       AL138845      121558 bp     DNA             linear       HTG
21-DEC-2001
DEFINITION  Homo sapiens chromosome 1 clone RP4-781A20 map p32.1-32.3, ***
            SEQUENCING IN PROGRESS ***, 17 unordered pieces.
ACCESSION   AL138845
VERSION     AL138845.7 GI:12539482
KEYWORDS    HTG HTGS_PHASE1.
SOURCE      Homo sapiens.
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
Euteleostomi;
            Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 0 to 0)
  AUTHORS   Plumb,B.
  TITLE     Direct Submission
  JOURNAL   Submitted (11-DEC-2001) Wellcome Trust Sanger Institute,
            Hinxton,Cambridgeshire, CB10 1SA, UK. E-mail enquiries:
            humquery@sanger.ac.uk Clone requests: clonerequest@sanger.ac.uk
COMMENT     On Jan 25, 2001 this sequence version replaced gi:9796256.
.........................

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