[EMBOSS] showalign: maintain numbering of the reference sequence

[Peter Rice]

Dear Ingo,

On 16/04/2010 10:18, Ingo P. Korndoerfer wrote:
> dear fellow emboss users,
>
> who can help me out with this one:
>
> we URGENTLY need some commandline driven program, that nicely displays
> emma output, BUT MAINTAINS the sequence numbering of the reference sequence.

Interesting. Emma output is just a multiply aligned sequence file in any 
format.

> showalign seems to simply start counting at the first residue, even if
> it is a construct with just a purification tag, and happily includes
> alignment gaps in the numbering.

Showalign is the obvious application to update.

> this makes it real difficult for us to find a certain residue of a
> protein in our alignment, particularly important if the whole team wants
> to discuss certain details ...
>
> i have tried the refseq keyword, but that did not seem to do that ...

We can change that. Refseq is used to make one sequence appear first and be 
used to control numbering too. The ouptut of showalign is a text file (it 
does not write out an align object) so we are free to modify it.

The easiest is to add an option to number by the reference sequence when 
the ruler appears.

We can also add a test for a sequence ID matching without being case 
sensitive to make the -refseq option easier to use.

> any ideas, i'd be happy. would be nice if it were in emboss, since that
> is installed on all machines already, but if need to, we can install
> additional software ...

Happy to help. If you can give some examples of what you would like we can 
send you a version to test and then add it to the July release.

regards,

Peter Rice