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:
[EMAIL PROTECTED] Clone requests: [EMAIL PROTECTED]
COMMENT On Jan 25, 2001 this sequence version replaced gi:9796256.
.........................
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