[EMBOSS] emma: problem with filename : please help

[Peter Rice]

Charles Plessy wrote:
> Le Wed, Apr 16, 2008 at 10:40:33AM -0400, Duhaime Johanne a écrit :
>>  CLUSTAL W 2.0 Multiple Sequence Alignments
>>
>>
>> Error: parameter required for /dnamatrix
> 
> Hello,
> 
> apparently, emma passes an empty '-dnamatrix=' argument that is accepted
> by clustalw 1.83, but not 2.0. I do not know if it is a regression in
> clustalw or a problem of emma.

Ah, many thanks. Clustalw may be happy, but that is a bug. Clustalw 1.83
defaults to the correct matrix but does not complain about the
incomplete commandline qualifier.

With this fixed, emma appears to work well with later versions of
clustalw ... but we would need to check the results and look for any
similar problems that show up only in the 2.0 clustalw release..

In emma.c the wrong characters are tested.

release 5.0.0:
     if(m2c=='b')
	ajStrAssignC(&m2str,"iub");
     else if(m2c=='p')
	ajStrAssignC(&m2str,"clustalw");
     else if(m2c=='g')
	ajStrAssignC(&m2str,"own");

corrected:
     if(m2c=='i')
	ajStrAssignC(&m2str,"iub");
     else if(m2c=='c')
	ajStrAssignC(&m2str,"clustalw");
     else if(m2c=='o')
	ajStrAssignC(&m2str,"own");

regards,

Peter