[EMBOSS] emma

[Staffa, Nick (NIH/NIEHS)]

Thanks, but
Your comment 
> They are now :-)
is cryptic.

Our emma.c (/EMBOSS-5.0.0) has this:

dna_matrix = ajAcdGetListSingle( "dnamatrix");
m2c = ajStrGetCharFirst(dna_matrix);
 
if(m2c=='b')
       ajStrAssignC(&m2str,"iub");else if(m2c=='p')
ajStrAssignC(&m2str,"clustalw");
else if(m2c=='g')
    ajStrAssignC(&m2str,"own");

Should we change the if "m2c==" tests to conform to your i,c,o
and recompile?


On 5/15/08 3:27 AM, "Peter Rice" <pmr at ebi.ac.uk> wrote:

> Staffa, Nick (NIH/NIEHS) wrote:
>> ******** CLUSTAL 2.0.7 Multiple Sequence Alignments  ********
>> 
>> Command line emma in conjunction with this program generates this error:
>> 
>> CLUSTAL 2.0.7 Multiple Sequence Alignments Error: parameter
>> required for /dnamatrix Error: Failed to open filename '00003189B'
> 
> There is a bug in emma, not noticed before because Clustalw 1.x
> tolerated the command line.
> 
> In emboss/emma.c the code for option dnamatrix should be:
> 
>      dna_matrix = ajAcdGetListSingle( "dnamatrix");
>      m2c = ajStrGetCharFirst(dna_matrix);
> 
>      if(m2c=='i')
>          ajStrAssignC(&m2str,"iub");
>      else if(m2c=='c')
>          ajStrAssignC(&m2str,"clustalw");
>      else if(m2c=='o')
>          ajStrAssignC(&m2str,"own");
> 
> (the characters tested for m2c were from another command line option so
> the dnamatrix option was not being passed to clustalw).
> 
> Clustalw 1.8.x ignored the empty /dnamatrix string on the commmand line.
> 
>> Y'd think the defaults would be sufficient.
> 
> They are now :-)
> 
>> Y'd think that Jemboss would do a better job of reporting problems.
> 
> It is always tricky when the error is reported by another application
> invoked through EMBOSS.
> 
> My favourite emma error was a Taverna workflow that failed when
> executing an emma webservice. Clustalw crashed. The cause turned out to
> be a user-generated FASTA file with bad end of line characters in the
> sequence so the sequences became part of the first ID and emma launched
> clustalw with a set of zero length sequences. We "fixed" it by requiring
> all EMBOSS sequences to have at least one valid character so we can now
> issue an EMBOSS error.
> 
> regards,
> 
> Peter