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hdx_peptide_gnuplot.sh
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hdx_peptide_gnuplot.sh
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#!/bin/bash
#check input
if [ -z $4 ] ; then
echo
echo 'Script to plot ms peptide spectra'
echo
echo "Usage ${0##*/} (1) (2) (3) (4) ..."
echo ''
echo '(1) peptide name/label (no spaces)'
echo '(2) min m/z value'
echo '(3) max m/z value'
echo '(4) data file(s) ending with .dat'
echo
echo 'exiting now...'
echo
exit
fi
PEPTIDE=$1
shift
RANGE_LOW=$1
shift
RANGE_HIGH=$1
shift
DATA=$*
#determine max y-value
#YMAX=`cat $DATA | awk '{print $i3}' | sort -g | tail -1 | awk '{print $1*1.1}'`
DATE=`date +%F | sed -e 's/-//g'`
SCRIPT=${DATE}_hdx-peptide_gnuplot.sh
for f in $DATA
do
echo \#\!'/bin/bash' > $SCRIPT
echo '' >> $SCRIPT
echo '' >> $SCRIPT
echo 'gnuplot -persist <<EOF' >> $SCRIPT
echo ' set term post color landscape' >> $SCRIPT
echo " set output" \""${DATE}_${f%*.dat}_${PEPTIDE}.eps"\" >> $SCRIPT
echo " unset key" >> $SCRIPT
echo " set title" \""${f%*.dat} ${PEPTIDE}"\" >> $SCRIPT
echo " set xrange[$RANGE_LOW:$RANGE_HIGH]" >> $SCRIPT
echo " set xtics nomirror out" >> $SCRIPT
echo " unset ytics" >> $SCRIPT
echo " set border 1 " >> $SCRIPT
echo " set yrange[0:*]" >> $SCRIPT
echo " set xlabel" \""m/z"\" >> $SCRIPT
echo " plot '$f' u 1:2 w l lc rgb " \""#000000"\" >> $SCRIPT
echo ' exit' >> $SCRIPT
echo 'EOF' >> $SCRIPT
echo 'exit' >> $SCRIPT
chmod +x $SCRIPT
./$SCRIPT
done
rm -f $SCRIPT
exit