IUBio

Seqlab extensions

Tim Cutts tjrc1 at mole.bio.cam.ac.uk
Wed Feb 18 12:39:54 EST 1998


Is it my imagination, or is writing Seqlab extensions so obtuse as to be
virtually impossible?

I am trying to write a seqlab extension so that people can use it to launch
fasta searches using Pearson's FASTA 3.0 (the parallel version).  Has
anyone already done this?  If not I will continue battling on...

Everything was going swimmingly until I tried implementing rules so that
the databases/fasta varieties the user could choose from would depend on
what sequence type/fasta variety they were choosing.

For example, if they choose fasta, I want it to only show them nucleic acid
databases if the query sequence is also nucleic.

So, I have things like:

SQChanges @DB, @100, @1, @3, @4, @5, @A, @O, @P

SQInfile *
  NucRules = -3, -5
  ProtRules = +3, +5
End

A bit later, there is the menu for the fasta program types:

  Menu
    id = 100
    menutype = 1
    columns = 4
    method = value
    qualifier = FPRG
    Bool
      id = 1
      prompt = fasta
      qualifier = fasta
      rules = nuc ? +A : -A, nuc ? -O : +O, nuc ? -P : +P
      method = name
    End
    Bool
      id = 3
      prompt = tfasta
      qualifier = tfasta
      rules = +A, -O, -P
      method = name
    End

etc.
.
.
.
  End 

And later still, the databases menu:

  Menu
    id = DB
    method = value
    prompt = "Database(s) to search"
    Bool
      id = A
      prompt = GENEMBL
      qualifier = A
      default = +
      method = name
    End
    Bool
      id = O
      prompt = TREMBL
      qualifier = O
      default = +
      method = name
    End
    Bool
      id = P
      prompt = OWL
      qualifier = P
      default = +
      method = name
    End
  End

As far as I can tell, this is all right, but there are numerous problems. 
For example, when I have a DNA sequence selected, the tfasta radio button
still appears, despite the SQInfiles NucRules line.  Why might this be?

Thanks for any help anyone can give me.

Regards,

Tim Cutts



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