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1 #!/usr/bin/env bash
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2 CSV=$1
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3 TH=$2
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4
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5 if [ $# -ne 2 ]; then
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6 echo " ==== ERROR ... you called this script inappropriately."
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7 echo ""
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8 echo " usage: $0 <index.csv> <threshold>"
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9 echo ""
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10 exit -1
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11 fi
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12
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13
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14 BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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15
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16 # get first genome in list (they are sorted)
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17 currgenome=$(tail -n +2 "$CSV" | head -1 | awk -F "," '{print $6}')
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18
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19 # fill array of chromosomes similarity
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20
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21 array=()
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22 arraytosort=()
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23 names=()
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24 homologies=()
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25 condition=0
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26 othergencounter=0
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27 # for problems with chromo X and Y
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28 highest=1
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29 # For all lines
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30
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31 cat $CSV | tail -n +2 > $1.temp
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32
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33 while IFS= read -r i
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34 do
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35
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36 othergenome=$(echo "$i" | awk -F "," '{print $6}')
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37 if [ "$condition" -eq 0 ]; then
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38 currgenome=$othergenome
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39 condition=1
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40 fi
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41
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42 if [ "$othergenome" != "$currgenome" ]; then
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43
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44 # Sort the array with temporal values
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45 #printf '%s\n' "${arraytosort[@]}"
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46 #echo "name is $currgenome"
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47
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48 sorted=($(printf '%s\n' "${arraytosort[@]}"|sort))
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49
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50 #echo "For chroomo $currgenome we have "
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51 #echo $(printf '%s,' "${sorted[@]}")
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52 # accumulate sum until threshold is reached
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53 usedValues=1
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54 usedValuesNext=2
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55 first=${sorted[0]}
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56 next=${sorted[${usedValues}]}
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57 nextofnext=${sorted[${usedValuesNext}]}
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58 finalvalue=$first
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59 divisor=0
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60 currdiff=$(LC_NUMERIC=POSIX awk -v a="$next" -v b="$nextofnext" 'BEGIN {print b-a }')
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61 TH=$(printf '%4.6f' $TH)
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62 #echo "$(LC_NUMERIC=POSIX awk -v a="$currdiff" -v b="$TH" 'BEGIN { printf("comp %f > %f = %d",a,b,a>b)} ')"
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63 condition=$(LC_NUMERIC=POSIX awk -v a="$currdiff" -v b="$TH" 'BEGIN { printf("%d",a>b)} ')
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64 #echo "first $first next $next result $currdiff condition $condition divisor $divisor th $TH finalvalue $finalvalue"
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65 while [ $condition -eq 1 -a $usedValuesNext -lt ${#sorted[@]} ];
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66 do
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67 usedValues=`expr $usedValues + 1`
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68 usedValuesNext=`expr $usedValuesNext + 1`
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69 finalvalue=$(LC_NUMERIC=POSIX awk -v a="$finalvalue" -v b="$next" 'BEGIN {print (a+b)}')
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70 next=${sorted[${usedValues}]}
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71 nextofnext=${sorted[${usedValuesNext}]}
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72
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73 currdiff=$(LC_NUMERIC=POSIX awk -v a="$nextofnext" -v b="$next" 'BEGIN {printf("%f", b-a) }')
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74 condition=$(LC_NUMERIC=POSIX awk -v a="$currdiff" -v b="$TH" 'BEGIN { printf("%d", a>b)} ')
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75 divisor=$(LC_NUMERIC=POSIX awk -v a="$divisor" 'BEGIN {print a+0.1}')
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76
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77 done
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78
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79 #echo "so this is what we got $finalvalue, when divided using $divisor"
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80
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81 # array holds the results
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82 #array[$highest]=$(awk -v a="$currsum" -v b="$othergencounter" 'BEGIN {print a/b}')
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83 finalvalue=$(LC_NUMERIC=POSIX awk -v a="$finalvalue" -v b="$usedValues" -v c="$divisor" 'BEGIN {printf("%f", a/(b-c))}')
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84 array[$highest]=$finalvalue
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85 homologies[$highest]=$usedValues
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86
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87 highest=`expr $highest + 1`
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88 condition=0
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89 names+=($currgenome)
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90 othergencounter=0
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91 unset arraytosort
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92
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93
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94
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95
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96 getvalue=$(echo "$i" | awk -F "," '{print $8}')
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97 # Copy value to array
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98 arraytosort[$othergencounter]=$getvalue
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99 #currsum=$(awk -v a="$currsum" -v b="$getvalue" 'BEGIN {print a=a+(1-b); exit}')
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100 othergencounter=`expr $othergencounter + 1`
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101 else
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102 getvalue=$(echo "$i" | awk -F "," '{print $8}')
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103 # Copy value to array
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104 arraytosort[$othergencounter]=$getvalue
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105 #currsum=$(awk -v a="$currsum" -v b="$getvalue" 'BEGIN {print a=a+(1-b); exit}')
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106 othergencounter=`expr $othergencounter + 1`
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107
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108 fi
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109
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110 done < "$1.temp"
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111
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112 # do the last!!!
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113 #if [ "$lastprint" == "$currgenome" ]; then
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114 # Sort the array with temporal values
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115 sorted=($(printf '%s\n' "${arraytosort[@]}"|sort))
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116
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117 usedValues=1
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118 usedValuesNext=2
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119 first=${sorted[0]}
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120 next=${sorted[${usedValues}]}
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121 nextofnext=${sorted[${usedValuesNext}]}
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122 finalvalue=$first
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123 divisor=0
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124 currdiff=$(LC_NUMERIC=POSIX awk -v a="$next" -v b="$nextofnext" 'BEGIN {print b-a }')
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125 TH=$(printf '%4.6f' $TH)
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126 #echo "$(LC_NUMERIC=POSIX awk -v a="$currdiff" -v b="$TH" 'BEGIN { printf("comp %f > %f = %d",a,b,a>b)} ')"
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127 condition=$(LC_NUMERIC=POSIX awk -v a="$currdiff" -v b="$TH" 'BEGIN { printf("%d",a>b)} ')
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128 #echo "first $first next $next result $currdiff condition $condition divisor $divisor th $TH finalvalue $finalvalue"
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129 while [ $condition -eq 1 -a $usedValuesNext -lt ${#sorted[@]} ];
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130 do
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131 usedValues=`expr $usedValues + 1`
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132 usedValuesNext=`expr $usedValuesNext + 1`
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133 finalvalue=$(LC_NUMERIC=POSIX awk -v a="$finalvalue" -v b="$next" 'BEGIN {print (a+b)}')
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134 next=${sorted[${usedValues}]}
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135 nextofnext=${sorted[${usedValuesNext}]}
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136
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137 currdiff=$(LC_NUMERIC=POSIX awk -v a="$nextofnext" -v b="$next" 'BEGIN {printf("%f", b-a) }')
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138 condition=$(LC_NUMERIC=POSIX awk -v a="$currdiff" -v b="$TH" 'BEGIN { printf("%d", a>b)} ')
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139 divisor=$(LC_NUMERIC=POSIX awk -v a="$divisor" 'BEGIN {print a+0.1}')
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140
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141 done
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142
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143 #echo "so this is what we got $finalvalue, when divided using $divisor"
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144
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145 # array holds the results
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146 #array[$highest]=$(awk -v a="$currsum" -v b="$othergencounter" 'BEGIN {print a/b}')
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147 finalvalue=$(LC_NUMERIC=POSIX awk -v a="$finalvalue" -v b="$usedValues" -v c="$divisor" 'BEGIN {printf("%f", a/(b-c))}')
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148 array[$highest]=$finalvalue
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149 homologies[$highest]=$usedValues
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150
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151
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152 highest=`expr $highest + 1`
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153 currsum=0
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154 names+=($currgenome)
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155 currgenome=$othergenome
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156 othergencounter=0
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157 #fi
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158
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159
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160 highest=`expr $highest - 1`
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161 rm $1.temp
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162
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163 tsum=0
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164 echo "deleteme" > $1.inter
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165 rm $1.inter
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166 aux=0
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167 for ((i = 1; i <= highest; i++)); do
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168 echo "${names[${aux}]} ${array[${i}]} ${homologies[${i}]}" >> $1.inter
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169 #echo "${names[${aux}]} ${array[${i}]} ${homologies[${i}]}"
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170 aux=`expr $aux + 1`
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171 #val=${array[${i}]}
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172 #tsum=$(awk -v a="$tsum" -v b="$val" '{print a=a+b}')
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173 done
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174
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175 #awk -v a="$tsum" b="$highest" '{print a/b}'
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176
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177 #sumfirst=$(awk -F "," 'BEGIN{suma=0}{suma = suma + $8}END{print suma}' "$CSV")
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178 #echo "$sumfirst"
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179
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180
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181
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