[EMBOSS] fparse - wEMBOSS input format issues

[Peter Rice]

khayeni wrote:
>         Error: Bad discrete states file 'sample.dat': read 10 states for
>         'Alpha',
>         expected 6
>         Error: Unable to read discrete states from 'sample.dat'
>         Died: fpars terminated: Bad value for '-infile' with -auto
>         defined
>         fpars exited with status 1...
>         
>         What could be the reason for this?
>         
>         The user also stated that when using a Windows based stand alone
>         implementation of the pars program the input file worked fine. 

In the EMBOSS port, we define for each program the characters that can be 
accepted. Unfortunately fpars is by default reading 0 and 1 only.

It should work the same way as the standalone pars if you edit 
emboss_acd/fpars.acd and add a line to the definition of the input file:

   discretestates: infile [
     parameter: "Y"
     characters: "\S+"
     help: "File containing one or more data sets"
   ]

You will need to reinstall the phylipnew programs (or copy the fpars.acd file to 
where the installed copy is, in share/EMBOSS/acd where EMBOSS and phylipnew were 
installed)

We intended characters: "" to have the same effect but it is not working in 
EMBOSS 4.1.0. \S+ is the internal representation for "any non-space character".

We will fix this - and fix the error message you saw - in the next release.

regards,

Peter Rice