Re: [MUMmer-help] delta to tsv

[Adam P. <aph...@gm...>]

Hi Anaïs,
No, there is not an easy way to go from a comma or tab separated file back
to a delta file. The delta format contains alignment information that is
not included in the output of show-coords. However, it would be possible to
edit the delta file itself using a custom script. You could look at this
file to identify the self matches, and remove only those records from the
delta file. The delta file format is described here:
http://mummer.sourceforge.net/manual/#nucmer

Sorry that I cannot think of an easier way to do what you want. Perhaps I
can implement this as a filter for a future version of delta-filter.

Best,
-Adam



On Tue, May 13, 2014 at 12:12 PM, Anais Gouin <ana...@ir...> wrote:

> Hello,
>
> I would like to know if it is possible to get a delta file from a tsv file?
> Actually, I  did a nucmer analysis, matching a fasta file against itself.
> Than I would like to filter the results using data-filter -m
> but the -m option will report only the matches corresponding to each
> sequence against itself. So I was thinking to get the tsv file
> from the delta one using show-coord, then delete all lines corresponding
> to undesirable matches (a sequence against itself) and
> then come back to a delta file to use data-filter.
> Is there a solution?
> Thanks,
>
> Anaïs
>
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> Anaïs GOUIN
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