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1 #!/bin/bash
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2
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3 FL=1000 # frequency limit
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4
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5 if [ $# != 8 ]; 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: $0 seqXName seqYName lenght similarity WL fixedL output.frags output.csv"
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9 echo ""
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10 exit -1
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11 fi
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12
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13 #{
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14
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15
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16 MYRAND=$((( RANDOM % 10000000) +1))
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17 MGDIR=${PWD}/${MYRAND}
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18 echo "MGDIR $MGDIR"
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19 mkdir -p ${MGDIR}
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20
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21 genoXname=$(basename "$1")
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22 genoYname=$(basename "$2")
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23 genoXname="${genoXname%.*}"
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24 genoYname="${genoYname%.*}"
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25
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26
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27 cp $1 $MGDIR/${genoXname}.fasta
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28 cp $2 $MGDIR/${genoYname}.fasta
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29 mkdir -p ${MGDIR}/dictionaries
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30 mkdir -p ${MGDIR}/fragments
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31
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32 genoXExt="fasta"
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33 genoYExt="fasta"
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34
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35
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36
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37 BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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38
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39 length=${3}
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40 similarity=${4}
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41 WL=${5} # wordSize
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42 fixedL=${6}
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43 output=${7}
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44 csv=${8}
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45
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46 mkdir ${MGDIR}/intermediateFiles
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47
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48 mkdir ${MGDIR}/intermediateFiles/${genoXname}-${genoYname}
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49 mkdir ${MGDIR}/results
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50 mkdir ${MGDIR}/intermediateFiles/dictionaries
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51 mkdir ${MGDIR}/intermediateFiles/hits
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52
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53 # Copiamos los fastas
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54 ln -s ${MGDIR}/${genoXname}.${genoXname} ${MGDIR}/intermediateFiles/${genoXname}-${genoYname}
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55 ln -s ${MGDIR}/${genoYname}.${genoYname} ${MGDIR}/intermediateFiles/${genoYname}-${genoXname}
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56
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57 cd ${MGDIR}/intermediateFiles/${genoXname}-${genoYname}
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58
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59 ###############
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60
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61
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62
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63 echo "${BINDIR}/reverseComplement ${MGDIR}/${genoYname}.${genoXExt} ${genoYname}-revercomp.${genoYExt}"
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64 ${BINDIR}/reverseComplement ${MGDIR}/${genoYname}.${genoYExt} ${MGDIR}/${genoYname}-revercomp.${genoYExt}
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65
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66 if [[ ! -f ../dictionaries/${genoXname}.d2hP ]]; then
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67 echo "${BINDIR}/dictionary.sh ${MGDIR}/${genoXname}.${genoXExt} &"
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68 ${BINDIR}/dictionary.sh ${MGDIR}/${genoXname}.${genoXExt} &
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69 fi
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70
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71 if [[ ! -f ../dictionaries/${seqYName}.d2hP ]]; then
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72 echo "${BINDIR}/dictionary.sh ${MGDIR}/${genoYname}.${genoYExt} &"
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73 ${BINDIR}/dictionary.sh ${MGDIR}/${genoYname}.${genoYExt} &
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74 fi
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75
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76 if [[ ! -f ../dictionaries/${genoYname}-revercomp.d2hP ]]; then
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77 echo "${BINDIR}/dictionary.sh ${MGDIR}/${genoYname}-revercomp.${genoYExt} &"
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78 ${BINDIR}/dictionary.sh ${MGDIR}/${genoYname}-revercomp.${genoYExt} &
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79 fi
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80
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81 echo "Waiting for the calculation of the dictionaries"
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82
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83 for job in `jobs -p`
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84 do
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85 #echo $job
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86 wait $job
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87 done
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88
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89
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90
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91 mv ${genoXname}.d2hP ../dictionaries/
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92 mv ${genoXname}.d2hW ../dictionaries/
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93 mv ${genoYname}.d2hP ../dictionaries/
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94 mv ${genoYname}.d2hW ../dictionaries/
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95 mv ${genoYname}-revercomp.d2hP ../dictionaries/
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96 mv ${genoYname}-revercomp.d2hW ../dictionaries/
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97
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98
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99
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100 # Hacemos enlace simbolico
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101 ln -s ../dictionaries/${genoXname}.d2hP .
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102 ln -s ../dictionaries/${genoXname}.d2hW .
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103
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104 ln -s ../dictionaries/${genoYname}.d2hP .
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105 ln -s ../dictionaries/${genoYname}.d2hW .
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106
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107 ln -s ../dictionaries/${genoYname}-revercomp.d2hP .
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108 ln -s ../dictionaries/${genoYname}-revercomp.d2hW .
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109
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110 echo "${BINDIR}/comparison.sh ${MGDIR}/${genoXname}.${genoXExt} ${MGDIR}/${genoYname}.${genoYExt} ${length} ${similarity} ${WL} ${fixedL} f &"
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111 ${BINDIR}/comparison.sh ${MGDIR}/${genoXname}.${genoXExt} ${MGDIR}/${genoYname}.${genoYExt} ${length} ${similarity} ${WL} ${fixedL} f &
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112
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113 echo "${BINDIR}/comparison.sh ${MGDIR}/${genoXname}.${genoXExt} ${MGDIR}/${genoYname}-revercomp.${genoYExt} ${length} ${similarity} ${WL} ${fixedL} r &"
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114 ${BINDIR}/comparison.sh ${MGDIR}/${genoXname}.${genoXExt} ${MGDIR}/${genoYname}-revercomp.${genoYExt} ${length} ${similarity} ${WL} ${fixedL} r &
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115
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116 echo "Waiting for the comparisons"
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117
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118 for job in `jobs -p`
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119 do
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120 #echo $job
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121 wait $job
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122 done
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123
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124
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125 #echo "rm ${seqYName}-revercomp.${extensionY}"
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126 #rm ${seqYName}-revercomp.${extensionY}
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127
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128
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129 echo "${BINDIR}/combineFrags ${genoXname}-${genoYname}-sf.frags ${genoXname}-${genoYname}-revercomp-sr.frags ${genoXname}-${genoYname}.frags"
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130 ${BINDIR}/combineFrags ${genoXname}-${genoYname}-sf.frags ${genoXname}-${genoYname}-revercomp-sr.frags ${genoXname}-${genoYname}.frags
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131
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132 #Borramos todo menos los frags y los diccionarios
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133
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134 # Get Info from frags
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135 echo "${BINDIR}/getInfo ${genoXname}-${genoYname}.frags > ${genoXname}-${genoYname}.csv"
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136 ${BINDIR}/getInfo ${genoXname}-${genoYname}.frags > ${genoXname}-${genoYname}.csv.tmp
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137 cat ${genoXname}-${genoYname}.frags.INF ${genoXname}-${genoYname}.csv.tmp > ${genoXname}-${genoYname}.csv
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138 rm -rf ${genoXname}-${genoYname}.csv.tmp
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139
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140 if [[ -L "../../${genoXname}.fasta" ]]
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141 then
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142 rm ../../${genoYname}.fasta
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143 fi
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144
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145 if [[ -L "../../${genoXname}.fasta" ]]
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146 then
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147 rm ../../${genoYname}.fasta
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148 fi
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149
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150 #Movemos los frags y los info
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151 mv ${genoXname}-${genoYname}.frags $output
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152 mv ${genoXname}-${genoYname}.csv $csv
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153
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154
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155
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156 #echo "Borrando ${seqXName}-${seqYName}"
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157 cd ..
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158
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159 #rm -rf ${seqXName}-${seqYName}
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160
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161 cd ..
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162
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163
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164 rm -r ${MGDIR}
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165
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