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
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