diff dnp-symmetrize.sh @ 0:b45de206654d draft default tip

"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dnp-symmetrize.sh	Fri May 01 12:08:23 2020 +0000
@@ -0,0 +1,73 @@
+#!/bin/sh
+
+if test "$#" -ne 2; then
+
+echo ""
+echo " CALL "  
+echo "   sh dnp-symmetrize.sh symmetrize-input.tabular symmetrize-output.tabular"
+echo ""
+echo " INPUT "
+echo "   symmetrize-input.tabular  - selected length dinucleotide frequency profiles from forward and complementary sequences"
+echo ""
+echo " OUTPUT "
+echo "   symmetrize-output.tabular - symmetrized output"
+echo ""
+echo " DESCRIPTION"
+echo "   Symmetrization of dinucleotide profiles reveals patterns with respect to nucleosome's dyad position."
+echo "   Frequency profiles of each dinucleotide derived from forward and complementary sequences are superimposed "
+echo "   with respect to a center of the dyad by averaging forward and reverse complement profiles at an identified"
+echo "   nucleosome's location. A first column contains position number relative to the dyad position."
+echo ""
+echo "   Example of an input table"
+echo "   pos    AA.f            AC.f            AG.f            AT.f            CA.f            CC.f            CG.f            CT.f     ..."
+echo "   20     0.100200        0.084720        0.077200        0.072480        0.066160        0.044160        0.004560        0.060720"
+echo "   21     0.172440        0.024800        0.002080        0.101240        0.131840        0.007200        0.000320        0.095920"
+echo "   22     0.077160        0.096240        0.314320        0.047360        0.012040        0.028560        0.011840        0.013680"
+echo "   ..."
+echo ""
+echo "   Example of a few columns of an output table"
+echo "   pos	AA	AC	AG	AT      ..."
+echo "   -73	0.08616	0.08034	0.07146	0.05934 ..."
+echo "   -72	0.11976	0.04966	0.03412	0.07274 ..."
+echo "   -71	0.07202	0.08882	0.18912	0.0462  ..."
+echo "   ... "
+
+    exit 1
+fi
+
+#
+# input file name
+name=$1
+# symmetrize all dinucleotides that are in the table
+
+# output file
+out=$2
+
+# compute centerd sequence position
+posi=`awk -v name=pos '{ for (i=1; i<=NF; i++) if($i==name) print i; exit}' ${name}`
+posnum=`awk -v k=${posi} '{print $k}' $name |head -n2| tail -n1`
+
+echo "pos" > positions
+awk -v k=${posi} '{print $k}' $name | tail -n +2 | awk -v offset=$((posnum-1)) '{print $1-offset-74}'>> positions
+
+
+# get the dinucleotides from the first line 
+dinucleotides=`head -n1 ${name} | sed 's/pos//' | sed 's/.f//g' | sed 's/.r//g'`  
+
+#cnum=1
+for di in ${dinucleotides}
+do
+    # column number for forward and complementary profile
+    i1=`awk -v name=$di'.f' '{ for (i=1; i<=NF; i++) if($i==name) print i; exit}' ${name}`
+    i2=`awk -v name=$di'.r' '{ for (i=1; i<=NF; i++) if($i==name) print i; exit}' ${name}`
+    awk -v k=${i1} '{print $k}' $name | grep -v ".f" > temp.${i1}
+    awk -v k=${i2} '{print $k}' $name | grep -v ".r" | tac > temp.${i2}
+    echo ${di} > cp.${di}
+   paste temp.${i1} temp.${i2} | awk '{print ($1+$2)/2 }' >> cp.${di}
+
+   #cnum=$((cnum+1))
+   
+done
+
+paste positions cp.* > ${out}
+rm temp* cp*  positions