Bonjour � tous,
J'ai un �trange probl�me avec gawk. Un script awk fonctionne bien sur
une SuSE 7.0 (gawk 3.0.5), mais pas sur SuSE 6.3 (gawk 3.0.4).
J'obtiens les erreurs suivantes:
user@ordi> signalp -t gram-
/BioInformatics/soft/bin/signalp-2.0/test/test.seq
gawk: /BioInformatics/soft/bin/signalp-2.0/bin/combine-nn.awk:40:
C[$1] /= nparts
gawk:
/BioInformatics/soft/bin/signalp-2.0/bin/combine-nn.awk:40:
^ parse error
gawk: /BioInformatics/soft/bin/signalp-2.0/bin/combine-nn.awk:42:
S[$1] /= nparts
gawk:
/BioInformatics/soft/bin/signalp-2.0/bin/combine-nn.awk:42:
^ parse error
Est-ce que des diff�rence dramatiques existent entre gawk 3.0.4 et
3.0.5??? De quel type d'erreur s'agit-il?
Merci d'avance,
Thierry.
--------La partie du combine-nn.awk qui pose probl�me est le suivant:
::::::::::::::
combine-nn.awk
::::::::::::::
#! /usr/bin/nawk -f
BEGIN {
nparts = 5 # No. of partitions to average over
nf = 6 # No. of fields in each partition file
if (format=="short") {
printf "# SignalP-NN %-50s\n", type " predictions"
print "# name Cmax pos ? "\
"Ymax pos ? Smax pos ? Smean ?"
}
}
NR=1 {
# The values in $TYPE.param have been read from the command line
# In gawk (a.o.) command line variable assignments has not taken
# effect in the BEGIN clause
split(Cscales, Cwt, ",")
}
/^ #/ {
N++
len = substr($0,39,6)+0
name = substr($0,7,20)
seq = ""
}
/SINGLE/ {
out=1
next
}
(out) {
C[$1] = S[$1] = 0
for (i=0; i<nparts; i++) {
C[$1] += $(nf*i+5) * Cwt[i+1]
S[$1] += $(nf*i+nf*nparts+5)
}
C[$1] /= nparts
if (C[$1]>1) C[$1]=1
S[$1] /= nparts
seq = seq $2
}
out && $1 == len {
out=0
datafile = datafileprefix "." N
if (format != "short") {
printf ">%s length = %d\n", name, len
printf ">%s length = %d\n\n", name, len > datafile
print "# pos aa C S Y" > datafile
}
Cmax = Smax = Ymax = 0
Cmaxpos = Smaxpos = Ymaxpos = 1
for (i=1-drange; i<=0; i++)
S[i]=S[1]
for (i=len+1; i<=len+drange; i++)
S[i]=S[len]
for (i=1; i<=len; i++) {
diff = 0
for (j= i-drange; j<i; j++)
diff += S[j]
for (j= i; j< i+drange; j++)
diff -= S[j]
diff /= drange
Y = (diff>0) ? sqrt(C[i]*diff) : 0
if (Y>Ymax) { Ymax=Y; Ymaxpos=i }
if (S[i]>Smax) { Smax=S[i]; Smaxpos=i }
if (C[i]>Cmax) { Cmax=C[i]; Cmaxpos=i }
if (format != "short") {
printf "%5d %1s %5.3f %5.3f %5.3f\n",
i, substr(seq,i,1), C[i], S[i], Y > datafile
}
}
close (datafile)
Smean = 0
for (i=start; i<=Ymaxpos-1; i++)
Smean += S[i]
if (Ymaxpos>1)
Smean /= (Ymaxpos - 1)
else
Smean = 0
if (format=="short") {
printf "%-10s ", name
printf "%5.3f %3d %1s ",
Cmax, Cmaxpos, (Cmax>Cmaxcut) ? "Y" : "N"
printf "%5.3f %3d %1s ",
Ymax, Ymaxpos, (Ymax>Ymaxcut) ? "Y" : "N"
printf "%5.3f %3d %1s ",
Smax, Smaxpos, (Smax>Smaxcut) ? "Y" : "N"
printf "%5.3f %1s\n",
Smean, (Smean>Smeancut) ? "Y" : "N"
next
}
printf "# Measure Position Value Cutoff signal peptide?\n"
printf " max. C %3d %5.3f %5.2f %s\n",
Cmaxpos, Cmax, Cmaxcut, (Cmax>Cmaxcut) ? "YES" : "NO"
printf " max. Y %3d %5.3f %5.2f %s\n",
Ymaxpos, Ymax, Ymaxcut, (Ymax>Ymaxcut) ? "YES" : "NO"
printf " max. S %3d %5.3f %5.2f %s\n",
Smaxpos, Smax, Smaxcut, (Smax>Smaxcut) ? "YES" : "NO"
printf " mean S 1-%-4d %5.3f %5.2f %s\n",
Ymaxpos-1, Smean, Smeancut, (Smean>Smeancut) ? "YES" : "NO"
if (Smax>Smaxcut || Ymax>Ymaxcut || Smean>Smeancut) {
printf "# Most likely cleavage site between pos. %d and %d: %s\n",
Ymaxpos-1, Ymaxpos,
substr(seq,Ymaxpos-3,3) "-" substr(seq,Ymaxpos,2)
}
print ""
}
--
http://www-internal.alphanet.ch/linux-leman/ avant de poser
une question. Ouais, pour se d�sabonner aussi.
