/usr/share/doc/transtermhp/examples/calibrate.sh is in transtermhp 2.09-3.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 | #!/bin/sh
#=============================
# Global Constants
#=============================
#HP_RANGE="-30 -2" # range of possible hp scores
#TAIL_RANGE="-7.15 -2" # range of possible tail scoress
NUM_BINS=25 # number of bins in the histogram
SAMPLESIZE=20000000 # length of random dna sequence to generate
#HP_RANGE="-25 -2" # range of possible hp scores
#TAIL_RANGE="-7 -2" # range of possible tail scoress
#NUM_BINS=10 # number of bins in the histogram
#SAMPLESIZE=200000 # length of random dna sequence to generate
# values for %AT that we generate data for:
AT="0.26 0.28 0.30 0.32 0.34 0.36 0.38"
AT="$AT 0.40 0.42 0.44 0.46 0.48 0.50 0.52 0.54 0.56 0.58"
AT="$AT 0.60 0.62 0.64 0.66 0.68 0.70 0.72 0.74 0.76 0.78"
AT="$AT 0.80 0.82 0.84"
#=============================
# Process commandline options
#=============================
if [ ${#} -lt 1 ] ; then
echo "usage: `basename $0` outputfile.dat [transterm options]" > /dev/stderr
exit 1
fi
output=$1
shift
#===========================
# Find helper scripts
#===========================
findprog() {
if [ -x "./$1" ] ; then
echo "./$1"
elif [ -x "`which $1`" ] ; then
echo "$1"
else
echo "`basename $0`: $1 must be in the current directory or on your PATH." > /dev/stderr
exit 2
fi
}
RAND=`findprog random_fasta.py`
TRANSTERM=`findprog transterm`
MAKE_EXPTERM=`findprog make_expterm.py`
#==============================
# Ensure python is avialable
#==============================
if [ ! -x "`which python`" ] ; then
echo "`basename $0`: python must be installed to run calibration scripts" > /dev/stderr
exit 3
fi
#=========================================
# Generate and calibrate on random data
#=========================================
rm -f random_terms.dat
echo "NOTE: warnings about 'using version 1.0 confidence' are expected and OK." > /dev/stderr
echo "TransTerm Options = " $*
$TRANSTERM $* --v1-conf -S -c 0 --all-context /dev/null /dev/null > /dev/stderr
for at in $AT ; do
echo "`basename $0`: Running TransTerm on random sequence with %AT = $at" > /dev/stderr
#================================
# Generate random DNA data
#================================
$RAND $at $SAMPLESIZE "random$at.fasta" "random$at.coords"
#==================================================
# Run Transterm on that random sequence
# output all terminators regardless of confidence
# in a striped down format
#==================================================
$TRANSTERM $* --v1-conf -S -c 0 "random$at.fasta" "random$at.coords" \
| awk '/TERM/ { print at, $9, $10 }' at=$at >> random_terms.dat
#=================================================
# Clean everything up
#=================================================
rm random$at.coords random$at.fasta
done
#===================================
# Make the actual expterms.dat file
#===================================
echo "Creating distribution file in $output" > /dev/stderr
$MAKE_EXPTERM random_terms.dat $SAMPLESIZE $NUM_BINS > $output
echo "-1" >> $output
$TRANSTERM $* -S -c 0 /dev/null /dev/null | grep -- "--" >> $output
echo "Done. You can run transterm with this background distribution using '-r $output'"
|