[Biojava-l] Writing Genbank files - again

[David Waring]

Note: I do get the sequence in the output file.

> -----Original Message-----
> From: biojava-l-admin@biojava.org [mailto:biojava-l-admin@biojava.org]On
> Behalf Of David Waring
> Sent: Thursday, January 24, 2002 6:10 PM
> To: biojava
> Subject: [Biojava-l] Writing Genbank files - again
>
>
> 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 and
> the feature
> (but no Feature tag). 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"
>
>
> 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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