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

"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dnp-compute-composite.sh	Fri May 01 12:08:23 2020 +0000
@@ -0,0 +1,77 @@
+#!/bin/sh
+
+if test "$#" -ne 2; then
+echo ""
+echo " CALL "
+echo "   sh dnp-compute-composite.sh compute-composite-input.tabular compute-composite-output.tabular"
+echo ""
+echo " INPUT "
+echo "   compute-composite-input.tabular  - dinucleotide frequency profiles containing all 16 dinucleotides"
+echo ""
+echo " OUTPUT "
+echo "   compute-composite-output.tabular - original input with WW SS RR YY columns added to the output"
+echo ""
+echo " DESCRIPTION"
+echo "   Composite dinucleotides weak/weak WW (A or T) , strong/strong SS (G or C), purine/purine RR (A or G), "
+echo "   and pyrimidine/pyrimidine YY (C or T) are generalized dinucleotide frequency patterns in nucleosome sequences."
+echo "   Given a tabular innput file with all 16 dinucleotides the composite patterns are computed as follows"
+echo "   WW=AA+AT+TA+TT, SS=CC+CG+GC+GG, RR=AG+GA+AA+GG, YY=CC+TT+CT+TC and their columns added to the original table."
+echo ""
+echo "   Example columns of an input 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 "   ... "
+echo "   Example columns of computed composites "
+echo "   ...   WW      SS      RR"
+echo "   ...   0.27644 0.1614  0.29494"
+echo "   ...   0.36788 0.1091  0.29428"
+echo "   ...   0.21406 0.12566 0.34432"
+echo "   ..."
+
+    exit 1
+fi
+
+name=$1
+out=$2
+
+## TO DO test that all required nucleotide columns are in file
+## if not, stop the execution
+
+# add the column of composite profile at the end
+## WW = AA+TT+AT+TA
+    i1=`awk '{ for (i=1; i<=NF; i++) if($i=="AA") print i; exit}' ${name}`
+    i2=`awk '{ for (i=1; i<=NF; i++) if($i=="AT") print i; exit}' ${name}`
+    i3=`awk '{ for (i=1; i<=NF; i++) if($i=="TA") print i; exit}' ${name}`
+    i4=`awk '{ for (i=1; i<=NF; i++) if($i=="TT") print i; exit}' ${name}`
+echo WW > ww
+cut -f${i1},${i2},${i3},${i4} ${name}| tail -n +2 | awk '{print $1+$2+$3+$4}' >> ww
+
+## SS = CC+CG+GC+GG
+    i1=`awk '{ for (i=1; i<=NF; i++) if($i=="CC") print i; exit}' ${name}`
+    i2=`awk '{ for (i=1; i<=NF; i++) if($i=="CG") print i; exit}' ${name}`
+    i3=`awk '{ for (i=1; i<=NF; i++) if($i=="GC") print i; exit}' ${name}`
+    i4=`awk '{ for (i=1; i<=NF; i++) if($i=="GG") print i; exit}' ${name}`
+echo SS > ss
+cut -f${i1},${i2},${i3},${i4} ${name}| tail -n +2 | awk '{print $1+$2+$3+$4}' >> ss
+ 
+## RR = AA+AG+GA+GG
+    i1=`awk '{ for (i=1; i<=NF; i++) if($i=="AA") print i; exit}' ${name}`
+    i2=`awk '{ for (i=1; i<=NF; i++) if($i=="AG") print i; exit}' ${name}`
+    i3=`awk '{ for (i=1; i<=NF; i++) if($i=="GA") print i; exit}' ${name}`
+    i4=`awk '{ for (i=1; i<=NF; i++) if($i=="GG") print i; exit}' ${name}`
+echo RR > rr
+cut -f${i1},${i2},${i3},${i4} ${name}| tail -n +2 | awk '{print $1+$2+$3+$4}' >> rr
+
+## YY = CC+CT+TC+TT
+    i1=`awk '{ for (i=1; i<=NF; i++) if($i=="CC") print i; exit}' ${name}`
+    i2=`awk '{ for (i=1; i<=NF; i++) if($i=="CT") print i; exit}' ${name}`
+    i3=`awk '{ for (i=1; i<=NF; i++) if($i=="TC") print i; exit}' ${name}`
+    i4=`awk '{ for (i=1; i<=NF; i++) if($i=="TT") print i; exit}' ${name}`
+echo YY > yy
+cut -f${i1},${i2},${i3},${i4} ${name}| tail -n +2 |awk '{print $1+$2+$3+$4}' >> yy
+
+paste ${name} ww ss rr yy > ${out}
+
+rm ww ss rr yy