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1 #!usr/bin/bash
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2
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3
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4 :<<'hey'
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5 Command line looks like this :
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6 ahopro_wrapper.sh ${ahopro_config} ${motif_file} ${function.function_selector} $outfile $function['seq_name'] $function['nbr_motif'] $actualN
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7 # if function = p-value :, commad line will looks like this :
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8 ahopro_wrapper.sh ${ahopro_config} ${motif_file} ${function.function_selector} $outfile $function['seq_name'] $function['nbr_motif'] $actualN ${letter_freq_file}
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9
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10
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11 hey
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12
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13 #sort out arguments
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14
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15 configfile=$1
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16 motif_file=$2
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17 function=$3
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18 #if function is "p-value", get the freqFile pramater
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19 if [ "$function" == "p-value" ] ; then
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20 letterFreqFile=$8
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21 fi
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22 output=$4
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23 SEQ_NAME=$5
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24 NBR_MOTIFS=$6
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25 actual_NBR=$7
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26
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27
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28
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29 PATH_AHOPRO="/usr/bin/ahopro/AhoPro.1.3/"
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30
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31
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32 # create tmp workindg dir and cd
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33
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34 OUTDIR=`mktemp -d`
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35
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36 #hard code the creation of OUTDIR
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37 if [ -d $OUTDIR ]; then
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38 chmod -R 777 $OUTDIR
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39 else
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40 mkdir $OUTDIR
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41 fi
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42
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43 chmod -R 777 $OUTDIR
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44
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45 cd $OUTDIR
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46
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47
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48
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49 #echo "######configfile out of XML form :" > $output
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50 #cat $configfile >> $output
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51 #echo "motifFile :" >> $output
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52 #cat $motif_file > $output
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53
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54
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55
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56
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57 ## ************ First, check if the number of actual motif is met in the entries. If not, warn, and quit ******************************************************
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58
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59 if [[ $NBR_MOTIFS != $actual_NBR ]]; then
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60
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61 cat <<doc >$output
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62 AhoPro error :
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63
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64 The number of motifs set in "Number of motifs" does not match the the actual number of motif entry in "Motifs" section. They should be the same.
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65
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66 Number of motifs : $NBR_MOTIFS
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67 Number of actual motif entered : $actual_NBR
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68
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69 Please recheck these parameters.
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70
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71 doc
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72
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73 exit 0
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74
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75 fi
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76
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77 ## ************ END check ******************************************************
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78
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79
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80
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81 ### **************** Deal with motif entery ****************************************************************************************************
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82
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83
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84 if [[ $NBR_MOTIFS = 1 ]]; then
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85
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86 #NO PARSING REQUIRED
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87
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88 #remove blank lines, tabs, spaces..
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89 cat $motif_file | awk '/^[0-9\-ACTGatgc]/ {print}' > motif_tmp_0.txt
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90 # reverse if the motif is a pmw, reverse it if necessary
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91 type=`cat motif_tmp_0.txt | awk ' END { if ($1 ~ /[acATGC]/) {print "words"} else {print "pmw"} }'`
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92
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93 if [[ "$type" == "pmw" ]]; then
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94
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95 NF=`cat motif_tmp_0.txt | awk ' END {print NF}'`
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96
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97 if [[ $NF != 4 ]]; then #if it's not vertical, reverse it
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98
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99 for ((c=1 ; c <= $NF; c++))
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100 do
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101 cat motif_tmp_0.txt | awk -v c=$c '{ printf $c" " } END {printf"\n"}' >> motif_0.txt
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102 done
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103
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104 rm motif_tmp_0.txt
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105
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106
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107 elif [[ $NF == 0 ]]; then
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108 echo "Please check the motif entries.Try removing tabulations, spaces." > $output
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109 exit 0
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110
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111 else #if vertical
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112 mv motif_tmp_0.txt motif_0.txt
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113 fi
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114
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115 else #if words
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116 mv motif_tmp_0.txt motif_0.txt
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117
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118 fi
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119
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120
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121 else # IF there is more than one motif
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122
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123 #check if it's true + parse motifs + warn
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124 N=`cat $motif_file | awk '/^[0-9\-ACTGatgc*]/ {print}' | awk ' BEGIN{RS="*"; n=0} {printf $0 > "motif_tmp_"n++} END {print n}'`
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125
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126 # reverse pmw (or not if it's vertical)
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127
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128 for ((i=0 ; i< $N ; i++))
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129 do
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130 # remove empty lines + check if it's a pmw, motif words.
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131 cat motif_tmp_$i | awk '/^[0-9\-ACTGatgc]/ {print}' > motif_tmp_tmp_$i
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132 type=`cat motif_tmp_tmp_$i | awk ' END { if ($1 ~ /[acATGC]/) {print "words"} else {print "pmw"} }'`
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133
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134 rm motif_tmp_$i
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135 # if pmw : check if it is horizontal, if so, reverse it (ahopro takes only vertical pmws !)
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136
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137 if [[ "$type" == "pmw" ]]; then
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138
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139 NF=`cat motif_tmp_tmp_$i | awk ' END {print NF}'`
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140
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141 if [[ $NF != 4 ]]; then #if it's not vertical, reverse it
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142
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143 for ((c=1 ; c <= $NF; c++))
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144 do
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145 cat motif_tmp_tmp_$i | awk -v c=$c '{ printf $c" " } END {printf"\n"}' >> motif_$i.txt
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146 done
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147 rm motif_tmp_tmp_$i
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148
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149
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150 elif [[ $NF == 0 ]]; then
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151 echo "Please check the motif entries, try removing tabulations, spaces." > $ouput
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152 exit 0
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153
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154 else #if vertical
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155 mv motif_tmp_tmp_$i motif_$i.txt
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156 fi
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157
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158 else #if words
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159 mv motif_tmp_tmp_$i motif_$i.txt
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160
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161 fi
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162
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163 #cat motif_$i.txt
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164 done
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165 fi
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166
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167 ## ****************************************** END motif entery treatment *********************************************************************************************************************
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168
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169 ###motif_0
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170 # next could be improved in bash (sed..)
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171
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172 #Add motif filenames to the configfile byt writing a new_config.txt (in CWD)
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173 ##but first, check what kind of correction ? basic : motifnames only ? or LetterFreqFile also ?
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174
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175 if [ "$function" == "p-value" ] ; then
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176
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177 python $PATH_AHOPRO/replaceLine.py $configfile "name_freq" $letterFreqFile
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178
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179 else
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180
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181 python $PATH_AHOPRO/replaceLine.py $configfile "name"
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182
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183 fi
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184
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185 ## get the new config file
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186 #new_config="$OUTDIR/new_config.txt"
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187 new_config="new_config.txt"
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188
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189 #echo "******** AhoPro Parameters ******** " >> $output
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190 #cat $new_config >> $output
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191 #call ahopro with config file
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192
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193
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194 #echo "******** AhoPro Results ******** " >> $output
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195
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196 $PATH_AHOPRO/ahokocc $new_config >> $output 2>&1
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197
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198 # improve line "Search in sequence .." with user entered sequence name (for more clarity). Do only if seq_name != 'X'
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199
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200 if [ "$SEQ_NAME" != "X" ] ; then
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201
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202 #remove sequence (if it exists)
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203 sed -i '/^Search/d' $output
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204 # add new line
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205 line="\nSearch in sequence : $SEQ_NAME\n"
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206 sed -i "1s/^/$line/" $output
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207
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208 fi
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209
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210 rm $new_config
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211
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