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annotate dnp-correlation-between-profiles.sh @ 0:448204d12325 draft default tip

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"planemo upload commit 1a32efb8343938e8d49190003f251c78b5a58225-dirty"
author erinija
date Fri, 01 May 2020 12:13:00 +0000
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1 #!/bin/sh
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2
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3 if test "$#" -ne 4; 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-correlation-between-profiles.sh difreq.tabular winsize dinucleotides correlations.tabular"
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8 echo ""
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9 echo " INPUT"
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10 echo " difreq.tabular - tabular file of dinucleotide frequencies on forward and complementary fasta sequences "
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11 echo " winsize - size of sliding window within which correlation is computed (default 146)"
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12 echo " dinucleotides - 'AA AC AG AT ...'"
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13 echo ""
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14 echo " OUTPUT"
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15 echo " correlations.tabular - tabular file of Pearson correlations at each position for given dinucleotides"
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16 echo ""
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17 echo " DESCRIPTION"
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18 echo " To find a position of highest symmetry between the"
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19 echo " dinucleotides positional frequency profiles on"
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20 echo " forward and complementary sequences a Pearson"
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21 echo " correlation coefficient is computed at each position"
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22 echo " between forward and complementary dinucleotide profiles"
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23 echo " within a sliding window."
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24 echo " Input file contains dinucleotide frequencies arranged in columns"
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25 echo " for input dinucleotides named by *.f and *.r corresponding to"
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26 echo " forward and complementary profiles as:"
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27 echo ""
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28 echo " AA.f AA.r AC.f AC.r AG.f AG.r"
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29 echo " 0.076320 0.067920 0.057800 0.078120 0.081600 0.061960"
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30 echo " 0.072540 0.069520 0.041800 0.079820 0.076300 0.055190"
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31 echo " ... ... ... ... ... ..."
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32 echo ""
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33 echo " The input.tabular file is output of a dnp-subset-dinuc-profile.sh script."
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34 echo " A tabular output file contains columns of correlation coefficients "
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35 echo " along the positions of the frequency profile. A first column labelled 0 contains "
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36 echo " average of all correlations at each position:"
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37 echo ""
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38 echo " 0 AA AC AG"
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39 echo " 0.042205 0.0882716 0.030175 0.126967 "
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40 echo " ... ... ... ..."
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41 echo ""
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42 echo " Position and value of maximum correlations"
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43 echo " of each dinucleotide are printed to a standard output."
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44 echo ""
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45 echo " REQUIREMENT"
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46 echo " dnp-corrprofile installed"
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47 echo " conda install -c bioconda dnp-corrprofile"
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48 echo ""
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49 exit 1
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50
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51 fi
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52
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53 name=$1
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54 window=$2
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55 dinucleotides=$3
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56 out=$4
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57
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58 call=dnp-corrprofile
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59
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60 # compute length of the file
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61 len=`wc ${name} |awk '{print $1}'`
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62 len=$((len-1))
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63
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64 for di in ${dinucleotides}
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65 do
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66 #extract column numbers of required dinucleotide
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67 i=`awk -v name=$di'.f' '{ for (i=1; i<=NF; i++) if($i==name) print i; exit}' $name`
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68
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69 # create a file of two columns in temp
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70 awk -v k1=${i} -v k2=$((i+1)) '{print $k1 "\t" $k2}' $name | sed -n "2,${len}p" > temp.${di}
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71
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72 # put the header of the column
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73 echo ${di} > cp${i}
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74
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75 # correlation dinucleotide profile along the sequence
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76 # ./corrprofile aa -n 219 -w 146
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77 # output in the temp column
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78 ${call} temp.${di} -n $((len-1)) -w ${window} >> cp${i}
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79 # print the maximum
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80 posval=`cat cp${i} | grep -v ${di} | cat -n | sort -k2,2n | tail -n1`
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81 echo ${di} ${posval} >> maxpos
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82
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83 done
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84
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85 paste cp[1-9]* > temp
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86
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87 # compute average correlation profile
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88 awk 'NR==2{next}
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89 {T=0;
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90 for(N=1; N<=NF; N++) T+=$N;
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91 T/=NF
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92 print T "\t" $0}' temp > ${out}
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93
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94 # find a position of the maximum and output it
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95 posval=`cat ${out}| awk '{print $1} ' | cat -n | sort -k2,2n | tail -n1`
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96 echo "avg " ${posval} >> maxpos
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97 cat maxpos | tr "\n" ,
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98
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99 rm temp* cp[1-9]* maxpos