Package fork.lib.bio.seq

Examples of fork.lib.bio.seq.FastaExporter.appendEntry()

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    FastaExporter fe= new FastaExporter(out);
    Iterator<GenomicRegion> it= gb.iterator();
    while(it.hasNext()){
        GenomicRegion gr= it.next();
        String seq= get.getSequence(gr);
        fe.appendEntry(new FastaEntry(gr.toUCSCFormat(), seq));
        String cseq = NucleotideSequenceParser.parseSequence(seq).complementary().toString();
        DirectionalGenomicRegion cgr= new DirectionalGenomicRegion(gr.chr, '-', (int)gr.low, (int)gr.high);
        fe.appendEntry(new FastaEntry( cgr.toUCSCFormat(), cseq));
    }
    fe.close();
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        GenomicRegion gr= it.next();
        String seq= get.getSequence(gr);
        fe.appendEntry(new FastaEntry(gr.toUCSCFormat(), seq));
        String cseq = NucleotideSequenceParser.parseSequence(seq).complementary().toString();
        DirectionalGenomicRegion cgr= new DirectionalGenomicRegion(gr.chr, '-', (int)gr.low, (int)gr.high);
        fe.appendEntry(new FastaEntry( cgr.toUCSCFormat(), cseq));
    }
    fe.close();
}

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