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annotate dnp-select-range.sh @ 0:611156829647 draft default tip

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"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author erinija
date Fri, 01 May 2020 12:07:46 +0000
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1 #!/bin/sh
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2
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3 if test "$#" -ne 5; then
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4 echo ""
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5 echo " CALL "
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6 echo " sh dnp-select-range.sh select-range-input.tabular start length dinucleotides select-range-output.tabular"
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7 echo ""
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8 echo " INPUT "
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9 echo " select-range-input.tabular - full length dinucleotide frequency profiles"
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10 echo " start - start position of selection - identified start position of nucleosome's sequence"
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11 echo " length - length of selection; default =146 nucleosome's length in base pairs"
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12 echo " dinucleotides - any subset of dinucleotides enclosed by quotes 'AA AC AG AT CA CC ...'"
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13 echo ""
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14 echo " OUTPUT "
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15 echo " select-range-output.tabular - rows of input file selected at a given position spanning a length"
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16 echo ""
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17 echo " DESCRIPTION"
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18 echo " Selects rows from input table within a given range and adds a column with a position number."
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19 echo ""
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20 echo " Example of an input table"
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21 echo " AA.f AA.r AC.f AC.r AG.f AG.r AT.f AT.r ..."
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22 echo " 0.0763 0.067920 0.057800 0.078120 0.081600 0.061960 0.055600 0.044080 ..."
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23 echo " 0.077160 0.073760 0.056000 0.072160 0.079400 0.060720 0.055960 0.047040 ..."
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24 echo " 0.083320 0.071200 0.053840 0.080760 0.084560 0.064880 0.050440 0.048720 ..."
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25 echo " 0.077960 0.068200 0.056040 0.075520 0.080120 0.061680 0.053160 0.047400 ..."
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26 echo " 0.078200 0.069120 0.056880 0.074000 0.084360 0.060840 0.053520 0.046280 ..."
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27 echo " ... "
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28 echo ""
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29 echo " Example of an output table where start=20"
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30 echo " pos AA.f AC.f AG.f AT.f CA.f CC.f CG.f CT.f ..."
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31 echo " 20 0.100200 0.084720 0.077200 0.072480 0.066160 0.044160 0.004560 0.060720 ..."
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32 echo " 21 0.172440 0.024800 0.002080 0.101240 0.131840 0.007200 0.000320 0.095920 ..."
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33 echo " 22 0.077160 0.096240 0.314320 0.047360 0.012040 0.028560 0.011840 0.013680 ..."
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34 echo " ..."
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35
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36 exit 1
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37 fi
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38
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39
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40 # input file name
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41 name=$1
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42
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43 # start position
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44 startpos=$2
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45
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46 # length of selection (146bp)
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47 length=$3
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48
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49 # list of dinucleotides
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50 dinucleotides=$4
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51
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52 # output file
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53 out=$5
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54
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55 # compute length of the file
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56 len=`wc ${name} |awk '{print $1}'`
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57 #echo $len
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58
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59 len=$((len-1))
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60
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61 # endpos
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62 endpos=$((startpos+length))
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63
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64 cnum=1
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65 # TO DO:should scheck if endpos is within the range
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66 for di in ${dinucleotides}
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67 do
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68 # column number for forward and complementary profile
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69 i1=`awk -v name=$di'.f' '{ for (i=1; i<=NF; i++) if($i==name) print i; exit}' ${name}`
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70 i2=`awk -v name=$di'.r' '{ for (i=1; i<=NF; i++) if($i==name) print i; exit}' ${name}`
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71
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72 echo "$di.f" > forward.${di}
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73 awk -v k=${i1} '{print $k}' $name | sed -n "${startpos},${endpos}p" >> forward.${di}
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74 echo "$di.r"> complement.${di}
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75 awk -v k=${i2} '{print $k}' $name | sed -n "${startpos},${endpos}p" >> complement.${di}
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76 cnum=$((cnum+1))
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77 done
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78
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79 # sequence positions within range
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80 echo "pos" > seq.pos
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81 seq ${startpos} 1 ${endpos} >> seq.pos
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82
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83 # paste forward
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84 paste seq.pos forward.* > forward
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85 paste complement.* > complement
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86
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87 # create output
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88 paste forward complement > ${out}
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89 rm seq.pos forward* complement*