Note: I do get the sequence in the output file. > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]]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: > [EMAIL PROTECTED] Clone requests: > [EMAIL PROTECTED] > COMMENT On Jan 25, 2001 this sequence version replaced gi:9796256. > ......................... > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l
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