Mercurial > repos > erinija > dnp_correlation_between_profiles

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

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"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author erinija
date Fri, 01 May 2020 12:08:23 +0000
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1 #!/bin/sh
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2
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3 if test "$#" -ne 2; then
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4
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5 echo ""
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6 echo " CALL "
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7 echo " sh dnp-symmetrize.sh symmetrize-input.tabular symmetrize-output.tabular"
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8 echo ""
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9 echo " INPUT "
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10 echo " symmetrize-input.tabular - selected length dinucleotide frequency profiles from forward and complementary sequences"
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11 echo ""
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12 echo " OUTPUT "
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13 echo " symmetrize-output.tabular - symmetrized output"
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14 echo ""
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15 echo " DESCRIPTION"
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16 echo " Symmetrization of dinucleotide profiles reveals patterns with respect to nucleosome's dyad position."
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17 echo " Frequency profiles of each dinucleotide derived from forward and complementary sequences are superimposed "
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18 echo " with respect to a center of the dyad by averaging forward and reverse complement profiles at an identified"
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19 echo " nucleosome's location. A first column contains position number relative to the dyad position."
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20 echo ""
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21 echo " Example of an input table"
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22 echo " pos AA.f AC.f AG.f AT.f CA.f CC.f CG.f CT.f ..."
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23 echo " 20 0.100200 0.084720 0.077200 0.072480 0.066160 0.044160 0.004560 0.060720"
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24 echo " 21 0.172440 0.024800 0.002080 0.101240 0.131840 0.007200 0.000320 0.095920"
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25 echo " 22 0.077160 0.096240 0.314320 0.047360 0.012040 0.028560 0.011840 0.013680"
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26 echo " ..."
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27 echo ""
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28 echo " Example of a few columns of an output table"
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29 echo " pos AA AC AG AT ..."
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30 echo " -73 0.08616 0.08034 0.07146 0.05934 ..."
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31 echo " -72 0.11976 0.04966 0.03412 0.07274 ..."
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32 echo " -71 0.07202 0.08882 0.18912 0.0462 ..."
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33 echo " ... "
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34
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35 exit 1
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36 fi
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37
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38 #
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39 # input file name
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40 name=$1
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41 # symmetrize all dinucleotides that are in the table
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42
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43 # output file
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44 out=$2
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45
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46 # compute centerd sequence position
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47 posi=`awk -v name=pos '{ for (i=1; i<=NF; i++) if($i==name) print i; exit}' ${name}`
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48 posnum=`awk -v k=${posi} '{print $k}' $name |head -n2| tail -n1`
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49
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50 echo "pos" > positions
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51 awk -v k=${posi} '{print $k}' $name | tail -n +2 | awk -v offset=$((posnum-1)) '{print $1-offset-74}'>> positions
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52
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53
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54 # get the dinucleotides from the first line
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55 dinucleotides=`head -n1 ${name} | sed 's/pos//' | sed 's/.f//g' | sed 's/.r//g'`
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56
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57 #cnum=1
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58 for di in ${dinucleotides}
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59 do
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60 # column number for forward and complementary profile
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61 i1=`awk -v name=$di'.f' '{ for (i=1; i<=NF; i++) if($i==name) print i; exit}' ${name}`
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62 i2=`awk -v name=$di'.r' '{ for (i=1; i<=NF; i++) if($i==name) print i; exit}' ${name}`
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63 awk -v k=${i1} '{print $k}' $name | grep -v ".f" > temp.${i1}
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64 awk -v k=${i2} '{print $k}' $name | grep -v ".r" | tac > temp.${i2}
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65 echo ${di} > cp.${di}
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66 paste temp.${i1} temp.${i2} | awk '{print ($1+$2)/2 }' >> cp.${di}
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67
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68 #cnum=$((cnum+1))
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69
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70 done
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71
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72 paste positions cp.* > ${out}
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73 rm temp* cp* positions