[Biojava-l] SubSequence Help

Richard Holland holland at eaglegenomics.com
Thu Nov 6 12:13:07 UTC 2008

I've just tried to reproduce this and haven't been able to.

Could you supply the full code, including the bit where you set
startCoord and endCoord, and also the full file that you're working on
it with?

(You'll have to send them direct to me if you're using attachments as
the mailing list won't accept them).


2008/11/6 Ella Veitch <ella.veitch at gmail.com>:
> Hi guys- new here hope this is the right medium for getting questions
> answered.
> I hope someone can shed some light as to what i am doing wrong here
> I am trying to extract subsequence data from a RichSequence as follows:
>        RichSequenceIterator seqs=RichSequence.IOTools.readFastaDNA(input,
> ns);
>        RichSequence rs=seqs.nextRichSequence();
>        return RichSequence.Tools.subSequence(rs, startCoord,
> endCoord,rs.getNamespace(),seqName,
>                                rs.getAccession(), rs.getIdentifier(),
> rs.getVersion(),rs.getSeqVersion());
> When I check my result againt the expected i find that for example 5001-5175
> yeilds a sequence located at 10001 and 10175
> Any insights as to why?
> I hope so
> Thanks for your help
> Ella
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Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com

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