Mercurial > repos > erinija > dnp_correlation_between_profiles

annotate dnp-compute-composite.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 echo ""
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5 echo " CALL "
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6 echo " sh dnp-compute-composite.sh compute-composite-input.tabular compute-composite-output.tabular"
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7 echo ""
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8 echo " INPUT "
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9 echo " compute-composite-input.tabular - dinucleotide frequency profiles containing all 16 dinucleotides"
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10 echo ""
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11 echo " OUTPUT "
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12 echo " compute-composite-output.tabular - original input with WW SS RR YY columns added to the output"
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13 echo ""
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14 echo " DESCRIPTION"
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15 echo " Composite dinucleotides weak/weak WW (A or T) , strong/strong SS (G or C), purine/purine RR (A or G), "
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16 echo " and pyrimidine/pyrimidine YY (C or T) are generalized dinucleotide frequency patterns in nucleosome sequences."
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17 echo " Given a tabular innput file with all 16 dinucleotides the composite patterns are computed as follows"
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18 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."
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19 echo ""
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20 echo " Example columns of an input table"
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21 echo " pos AA AC AG AT ..."
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22 echo " -73 0.08616 0.08034 0.07146 0.05934 ..."
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23 echo " -72 0.11976 0.04966 0.03412 0.07274 ..."
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24 echo " -71 0.07202 0.08882 0.18912 0.0462 ..."
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25 echo " ... "
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26 echo " Example columns of computed composites "
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27 echo " ... WW SS RR"
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28 echo " ... 0.27644 0.1614 0.29494"
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29 echo " ... 0.36788 0.1091 0.29428"
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30 echo " ... 0.21406 0.12566 0.34432"
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31 echo " ..."
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32
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33 exit 1
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34 fi
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35
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36 name=$1
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37 out=$2
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38
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39 ## TO DO test that all required nucleotide columns are in file
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40 ## if not, stop the execution
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41
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42 # add the column of composite profile at the end
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43 ## WW = AA+TT+AT+TA
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44 i1=`awk '{ for (i=1; i<=NF; i++) if($i=="AA") print i; exit}' ${name}`
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45 i2=`awk '{ for (i=1; i<=NF; i++) if($i=="AT") print i; exit}' ${name}`
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46 i3=`awk '{ for (i=1; i<=NF; i++) if($i=="TA") print i; exit}' ${name}`
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47 i4=`awk '{ for (i=1; i<=NF; i++) if($i=="TT") print i; exit}' ${name}`
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48 echo WW > ww
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49 cut -f${i1},${i2},${i3},${i4} ${name}| tail -n +2 | awk '{print $1+$2+$3+$4}' >> ww
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50
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51 ## SS = CC+CG+GC+GG
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52 i1=`awk '{ for (i=1; i<=NF; i++) if($i=="CC") print i; exit}' ${name}`
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53 i2=`awk '{ for (i=1; i<=NF; i++) if($i=="CG") print i; exit}' ${name}`
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54 i3=`awk '{ for (i=1; i<=NF; i++) if($i=="GC") print i; exit}' ${name}`
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55 i4=`awk '{ for (i=1; i<=NF; i++) if($i=="GG") print i; exit}' ${name}`
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56 echo SS > ss
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57 cut -f${i1},${i2},${i3},${i4} ${name}| tail -n +2 | awk '{print $1+$2+$3+$4}' >> ss
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58
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59 ## RR = AA+AG+GA+GG
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60 i1=`awk '{ for (i=1; i<=NF; i++) if($i=="AA") print i; exit}' ${name}`
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61 i2=`awk '{ for (i=1; i<=NF; i++) if($i=="AG") print i; exit}' ${name}`
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62 i3=`awk '{ for (i=1; i<=NF; i++) if($i=="GA") print i; exit}' ${name}`
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63 i4=`awk '{ for (i=1; i<=NF; i++) if($i=="GG") print i; exit}' ${name}`
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64 echo RR > rr
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65 cut -f${i1},${i2},${i3},${i4} ${name}| tail -n +2 | awk '{print $1+$2+$3+$4}' >> rr
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66
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67 ## YY = CC+CT+TC+TT
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68 i1=`awk '{ for (i=1; i<=NF; i++) if($i=="CC") print i; exit}' ${name}`
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69 i2=`awk '{ for (i=1; i<=NF; i++) if($i=="CT") print i; exit}' ${name}`
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70 i3=`awk '{ for (i=1; i<=NF; i++) if($i=="TC") print i; exit}' ${name}`
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71 i4=`awk '{ for (i=1; i<=NF; i++) if($i=="TT") print i; exit}' ${name}`
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72 echo YY > yy
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73 cut -f${i1},${i2},${i3},${i4} ${name}| tail -n +2 |awk '{print $1+$2+$3+$4}' >> yy
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74
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75 paste ${name} ww ss rr yy > ${out}
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76
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77 rm ww ss rr yy