[EMBOSS] Re: wemboss: warning and errors

[Martin Sarachu]

Dear Rani,

about the error with ACD, when running distmat from command line 
(-options to be prompted for all options) I get this error with ACD

> # distmat -options
> Creates a distance matrix from multiple alignments
> Input sequence set: uniprot:papa_*
> Multiple substitution correction methods for proteins
>          0 : Uncorrected
>          1 : Jukes-Cantor
>          2 : Kimura Protein
> Method to use [0]: 1
> Warning: ACD expression invalid @(!$acdprotein)
> 
> Warning: ACD expression invalid @(!$acdprotein)
> 
> Error: File /usr/local/emboss/share/EMBOSS/acd/distmat.acd line 60: (ambiguous) Bad additional flag N | Y)
> 

but without -options (i.e. default options chosen) runs ok

> # distmat
> Creates a distance matrix from multiple alignments
> Input sequence set: uniprot:papa_*
> Multiple substitution correction methods for proteins
>          0 : Uncorrected
>          1 : Jukes-Cantor
>          2 : Kimura Protein
> Method to use [0]: 1
> Output file [papa_.distmat]:
> Warning: Sequence lengths are not equal!
> Warning: Sequence lengths are not equal!
> Warning: Sequence lengths are not equal!

there is a missing left parenthesis in distmat.acd in line 61, please 
change this

>     additional: "@(@(@(!$acdprotein)) & @($(nucmethod)==1)) |

to this

>     additional: "@(@(@(!$(acdprotein)) & @($(nucmethod)==1)) |


Regards,

Martin

PS: working on the exclude problem...


Mamidipalli, SudhaRani (S) wrote:
> Hello Martin,
> 
> While testing the programs in wEMBOSS,we have encountered couple of problems.
> 
> 1.The 'distmat' program gave some warning. Here is the warning of that program. 
> -------------------------------
> Warning! 
> "ambiguous" parameter: syntax error (missing left parenthesis) in ACD expression (tell to EMBOSS Manager : this could produce wrong results from program execution!) 
> -------------------------------
> I went and checked distmat.acd file but couldn't find any error. 
> 
> 2. I added some programs, that we don't want to be displayed in wemboss, in the exclude file: /genomics/sw/wEMBOSS-1.4.0/wEMBOSS/data/exclude. And then I re-installed wrappers4EMBOSS and wEMBOSS. Surprisingly, only few programs(for example tranalign,embossversion etc.) got deleted from wemboss whereas few programs (for example textsearch, entret etc.) show up with error 
> --------
> EMBOSS: error...
> chaos has been excluded
> ----------
>   
> Please clarify.
> 
> Thanks and Regards,
> Rani.
> 

-- 
Martin Sarachu
msarachu at biol.unlp.edu.ar
AR.EMBnet
http://www.ar.embnet.org