Hi Thierry, good question about the gap file & column headers.
The first columns are as described by the file headers. The subsequent
columns come in triplets, one triplet for each aligned genome,
containing the following information:
1. The genomic position of the gap
2. The name of the chromosome where the gap is located
3. The contig-local position of the gap
I agree this is confusing and this information should be added to the
file headers in a future Mauve release.
As for your second question, there is currently no way to produce a
reordered GenBank format file with the contig mover.
If you've got automatically generated annotations, then if possible I
would suggest running the annotation after reordering contigs.
Best,
-Aaron
On Wed, 2016-10-12 at 17:09 +0200, Thierry K.S. Janssens wrote:
> Dear Dr. Darling/Aaron,
>
> I have a small question regarding the interpretation of the
> coordinates
> in the exported gap file.
> The headers in this tab delimited file is less than the nuber of
> colums.
> This makes the interpretation cumbersome.
>
> Could you also give a hint how to maintain the annotations in from
> the
> Genbank, beyond the first iteration of the contig reordering?
>
> Thank you in advance for a short explanation on this.
>
> kind regards,
>
> Thierry Janssens
>
>
>
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Aaron E. Darling, Ph.D.
Associate Professor, ithree institute
University of Technology Sydney
Australia
http://darlinglab.org
twitter: @koadman
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