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$Seq.trunc and $Seq.app in 5.1

K. Cuelenaere koenc at caos.kun.nl
Fri Feb 12 08:25:41 EST 1999


Hi there,

 perhaps these are problems already solved; if so, I'm afraid
I've missed it in this newsgroup.

It's about the split files:

the trunc c function wasn't ok: I changed the commented line (by me)
and now it works fine (this must have been already solved at
the other srs servers because they seem to "trunc" ok). However
the ftp-able distribution on ftp.ebi still contains the old SeqIopTrunc
function.

SEQv SeqIopTrunc (Int4 runTime, SEQv seq, Int4 l)
{
  if (runTime)
    IargGetArgs ("seq|len", &seq, &l);
/*  SeqSubSeq (seq, 1, SeqLen (seq)); oops, always returns the entire sequence*/
  SeqSubSeq (seq, 1,  SeqLen (seq) - l);
  IcaReturn ("Seq", seq);            
  return seq;
}

And about the use of $s.app in the embl.is (and others): I don't get it.
One should first do all the $s.app and finally a $s.make.
But in embl.is the $s.make is done in the seq production, which
can be called several times for one sequence when dealing with
split sequences.... So the result is (with our embl) that only the last
sequence part is returned. The same is achieved in an icarus test file:

$s.app:"abc"
$s.make
$s.app:"def"
$s.make 
$Print:$s.str

results in: "def"

 So, ok, one should use the make just after the
last app, but how come it works right with the other srs servers, while
I can't notice a difference with our embl.is file ... was there
also a change in the SeqIopApp c function? Most other srs servers
are dealing well with split entries, but e.g. BEN doesn't.

best regards,
Koen.
-- 
--------------------------------------------------------------
Koen Cuelenaere			Email: koenc at caos.kun.nl
CAOS/CAMM Center		Phone: +31 24 3653383
University of Nijmegen		Fax:   +31 24 3652977
Toernooiveld
6525 ED Nijmegen
The Netherlands			URL: http://www.caos.kun.nl/
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