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1 #!/bin/sh
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2 #
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3 # pal_finder_wrapper.sh: run pal_finder perl script as a Galaxy tool
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4 #
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5 # Usage: run_palfinder.sh FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY FILTERED_MICROSATS [OPTIONS]
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6 # run_palfinder.sh --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]
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7 #
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8 # Options:
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9 #
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10 # --primer-prefix PREFIX: prefix added to the beginning of all primer names (prPrefixName)
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11 # --2merMinReps N: miniumum number of 2-mer repeat units to detect (0=ignore units of this size)
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12 # --3merMinReps N
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13 # --4merMinReps N
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14 # --5merMinReps N
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15 # --6merMinReps N
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16 # --primer-mispriming-library FASTA: specify a Fasta file with sequences to avoid amplifying
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17 # --primer-opt-size VALUE: optimum primer length
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18 # --primer-min-size VALUE: minimum acceptable primer length
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19 # --primer-max-size VALUE: maximum acceptable primer length
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20 # --primer-min-gc VALUE: minimum allowable percentage of Gs and Cs in any primer
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21 # --primer-max-gc VALUE: maximum allowable percentage of Gs and Cs
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22 # --primer-gc-clamp VALUE: number of consecutive Gs and Cs at 3' end of both left and right primer
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23 # --primer-max-end-gc VALUE: max number of Gs or Cs in last five 3' bases of left or right primer
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24 # --primer-min-tm VALUE: minimum acceptable melting temperature (Celsius) for a primer oligo
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25 # --primer-max-tm VALUE: maximum acceptable melting temperature (Celsius)
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26 # --primer-opt-tm VALUE: optimum melting temperature (Celsius)
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27 # --primer-pair-max-diff-tm VALUE: max difference between melting temps of left & right primers
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28 # --output_config_file FNAME: write a copy of the config.txt file to FNAME
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29 # --filter_microsats FNAME: run Graeme Fox's Perl script to filter and sort the
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30 # microsatellites from pal_finder and write to FNAME
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31 #
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32 # pal_finder is available from http://sourceforge.net/projects/palfinder/
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33 #
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34 # primer3 is available from http://primer3.sourceforge.net/releases.php
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35 # (nb needs version 2.0.0-alpha)
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36 #
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37 # Explicitly set the locations of the pal_finder script, data files and the primer3
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38 # executable by setting the following variables in the environment:
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39 #
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40 # * PALFINDER_SCRIPT_DIR: location of the pal_finder Perl script (defaults to
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41 # /usr/bin)
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42 # * PALFINDER_DATA_DIR: location of the pal_finder data files (specifically
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43 # config.txt and simple.ref; defaults to /usr/share/pal_finder_v0.02.04)
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44 # * PRIMER3_CORE_EXE: name of the primer3_core program, which should include the
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45 # full path if it's not on the Galaxy user's PATH (defaults to primer3_core)
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46 #
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47 echo $*
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48 #
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49 # Initialise locations of scripts, data and executables
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50 #
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51 # Set these in the environment to overide at execution time
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52 : ${PALFINDER_SCRIPT_DIR:=/usr/bin}
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53 : ${PALFINDER_DATA_DIR:=/usr/share/pal_finder_v0.02.04}
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54 : ${PRIMER3_CORE_EXE:=primer3_core}
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55 #
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56 # Filter script is in the same directory as this script
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57 PALFINDER_FILTER_PL=$(dirname $0)/pal_finder_filter.pl
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58 if [ ! -f $PALFINDER_FILTER_PL ] ; then
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59 echo No pal_finder_filter.pl script >&2
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60 exit 1
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61 fi
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62 #
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63 # Check that we have all the components
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64 function have_program() {
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65 local program=$1
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66 local got_program=$(which $program 2>&1 | grep "no $(basename $program) in")
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67 if [ -z "$got_program" ] ; then
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68 echo yes
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69 else
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70 echo no
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71 fi
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72 }
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73 if [ "$(have_program $PRIMER3_CORE_EXE)" == "no" ] ; then
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74 echo "ERROR primer3_core missing: ${PRIMER3_CORE_EXE} not found" >&2
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75 exit 1
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76 fi
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77 if [ ! -f "${PALFINDER_DATA_DIR}/config.txt" ] ; then
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78 echo "ERROR pal_finder config.txt not found in ${PALFINDER_DATA_DIR}" >&2
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79 exit 1
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80 fi
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81 if [ ! -f "${PALFINDER_SCRIPT_DIR}/pal_finder_v0.02.04.pl" ] ; then
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82 echo "ERROR pal_finder_v0.02.04.pl not found in ${PALFINDER_SCRIPT_DIR}" >&2
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83 exit 1
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84 fi
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85 #
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86 # Initialise parameters used in the config.txt file
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87 PRIMER_PREFIX="test"
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88 MIN_2_MER_REPS=6
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89 MIN_3_MER_REPS=0
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90 MIN_4_MER_REPS=0
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91 MIN_5_MER_REPS=0
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92 MIN_6_MER_REPS=0
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93 PRIMER_MISPRIMING_LIBRARY=$PALFINDER_DATA_DIR/simple.ref
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94 PRIMER_OPT_SIZE=
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95 PRIMER_MAX_SIZE=
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96 PRIMER_MIN_SIZE=
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97 PRIMER_MAX_GC=
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98 PRIMER_MIN_GC=
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99 PRIMER_GC_CLAMP=
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100 PRIMER_MAX_END_GC=
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101 PRIMER_OPT_TM=
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102 PRIMER_MAX_TM=
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103 PRIMER_MIN_TM=
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104 PRIMER_PAIR_MAX_DIFF_TM=
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105 OUTPUT_CONFIG_FILE=
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106 FILTERED_MICROSATS=
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107 #
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108 # Collect command line arguments
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109 if [ $# -lt 2 ] ; then
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110 echo "Usage: $0 FASTQ_R1 FASTQ_R2 MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]"
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111 echo " $0 --454 FASTA MICROSAT_SUMMARY PAL_SUMMARY [OPTIONS]"
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112 exit
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113 fi
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114 if [ "$1" == "--454" ] ; then
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115 PLATFORM="454"
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116 FNA=$2
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117 else
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118 PLATFORM="Illumina"
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119 FASTQ_R1=$1
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120 FASTQ_R2=$2
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121 fi
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122 MICROSAT_SUMMARY=$3
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123 PAL_SUMMARY=$4
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124 shift; shift; shift; shift
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125 #
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126 # Collect command line options
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127 while [ ! -z "$1" ] ; do
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128 case "$1" in
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129 --primer-prefix)
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130 shift
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131 PRIMER_PREFIX=$1
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132 ;;
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133 --2merMinReps)
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134 shift
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135 MIN_2_MER_REPS=$1
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136 ;;
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137 --3merMinReps)
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138 shift
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139 MIN_3_MER_REPS=$1
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140 ;;
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141 --4merMinReps)
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142 shift
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143 MIN_4_MER_REPS=$1
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144 ;;
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145 --5merMinReps)
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146 shift
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147 MIN_5_MER_REPS=$1
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148 ;;
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149 --6merMinReps)
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150 shift
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151 MIN_6_MER_REPS=$1
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152 ;;
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153 --primer-mispriming-library)
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154 shift
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155 PRIMER_MISPRIMING_LIBRARY=$1
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156 ;;
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157 --primer-opt-size)
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158 shift
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159 PRIMER_OPT_SIZE=$1
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160 ;;
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161 --primer-max-size)
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162 shift
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163 PRIMER_MAX_SIZE=$1
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164 ;;
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165 --primer-min-size)
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166 shift
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167 PRIMER_MIN_SIZE=$1
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168 ;;
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169 --primer-max-gc)
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170 shift
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171 PRIMER_MAX_GC=$1
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172 ;;
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173 --primer-min-gc)
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174 shift
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175 PRIMER_MIN_GC=$1
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176 ;;
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177 --primer-gc-clamp)
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178 shift
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179 PRIMER_GC_CLAMP=$1
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180 ;;
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181 --primer-max-end-gc)
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182 shift
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183 PRIMER_MAX_END_GC=$1
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184 ;;
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185 --primer-opt-tm)
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186 shift
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187 PRIMER_OPT_TM=$1
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188 ;;
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189 --primer-max-tm)
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190 shift
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191 PRIMER_MAX_TM=$1
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192 ;;
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193 --primer-min-tm)
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194 shift
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195 PRIMER_MIN_TM=$1
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196 ;;
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197 --primer-pair-max-diff-tm)
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198 shift
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199 PRIMER_PAIR_MAX_DIFF_TM=$1
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200 ;;
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201 --output_config_file)
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202 shift
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203 OUTPUT_CONFIG_FILE=$1
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204 ;;
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205 --filter_microsats)
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206 shift
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207 FILTERED_MICROSATS=$1
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208 ;;
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209 *)
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210 echo Unknown option: $1 >&2
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211 exit 1
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212 ;;
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213 esac
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214 shift
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215 done
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216 #
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217 # Check that primer3_core is available
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218 got_primer3=`which $PRIMER3_CORE_EXE 2>&1 | grep -v "no primer3_core in"`
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219 if [ -z "$got_primer3" ] ; then
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220 echo ERROR primer3_core not found >&2
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221 exit 1
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222 fi
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223 #
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224 # Set up the working dir
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225 if [ "$PLATFORM" == "Illumina" ] ; then
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226 # Paired end Illumina data as input
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227 if [ $FASTQ_R1 == $FASTQ_R2 ] ; then
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228 echo ERROR R1 and R2 fastqs are the same file >&2
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229 exit 1
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230 fi
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231 ln -s $FASTQ_R1
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232 ln -s $FASTQ_R2
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233 fastq_r1=$(basename $FASTQ_R1)
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234 fastq_r2=$(basename $FASTQ_R2)
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235 else
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236 # 454 data as input
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237 ln -s $FNA
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238 fna=$(basename $FNA)
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239 fi
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240 ln -s $PRIMER_MISPRIMING_LIBRARY
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241 PRIMER_MISPRIMING_LIBRARY=$(basename $PRIMER_MISPRIMING_LIBRARY)
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242 mkdir Output
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243 #
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244 # Copy in the default config.txt file
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245 /bin/cp $PALFINDER_DATA_DIR/config.txt .
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246 #
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247 # Update the config.txt file with new values
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248 function set_config_value() {
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249 local key=$1
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250 local value=$2
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251 local config_txt=$3
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252 if [ -z "$value" ] ; then
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253 echo "No value for $key, left as default"
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254 else
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255 echo Setting "$key" to "$value"
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256 sed -i 's,^'"$key"' .*,'"$key"' '"$value"',' $config_txt
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257 fi
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258 }
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259 # Input files
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260 set_config_value platform $PLATFORM config.txt
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261 if [ "$PLATFORM" == "Illumina" ] ; then
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262 set_config_value inputFormat fastq config.txt
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263 set_config_value pairedEnd 1 config.txt
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264 set_config_value inputReadFile $fastq_r1 config.txt
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265 set_config_value pairedReadFile $fastq_r2 config.txt
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266 else
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267 set_config_value inputFormat fasta config.txt
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268 set_config_value pairedEnd 0 config.txt
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269 set_config_value input454reads $fna config.txt
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270 fi
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271 # Output files
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272 set_config_value MicrosatSumOut Output/microsat_summary.txt config.txt
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273 set_config_value PALsummaryOut Output/PAL_summary.txt config.txt
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274 # Microsat info
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275 set_config_value 2merMinReps $MIN_2_MER_REPS config.txt
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276 set_config_value 3merMinReps $MIN_3_MER_REPS config.txt
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277 set_config_value 4merMinReps $MIN_4_MER_REPS config.txt
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278 set_config_value 5merMinReps $MIN_5_MER_REPS config.txt
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279 set_config_value 6merMinReps $MIN_6_MER_REPS config.txt
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280 # Primer3 settings
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281 set_config_value primer3input Output/pr3in.txt config.txt
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282 set_config_value primer3output Output/pr3out.txt config.txt
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283 set_config_value primer3executable $PRIMER3_CORE_EXE config.txt
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284 set_config_value prNamePrefix ${PRIMER_PREFIX}_ config.txt
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285 set_config_value PRIMER_MISPRIMING_LIBRARY "$PRIMER_MISPRIMING_LIBRARY" config.txt
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286 set_config_value PRIMER_OPT_SIZE "$PRIMER_OPT_SIZE" config.txt
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287 set_config_value PRIMER_MIN_SIZE "$PRIMER_MIN_SIZE" config.txt
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288 set_config_value PRIMER_MAX_SIZE "$PRIMER_MAX_SIZE" config.txt
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289 set_config_value PRIMER_MIN_GC "$PRIMER_MIN_GC" config.txt
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290 set_config_value PRIMER_MAX_GC "$PRIMER_MAX_GC" config.txt
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291 set_config_value PRIMER_GC_CLAMP "$PRIMER_GC_CLAMP" config.txt
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292 set_config_value PRIMER_MAX_END_GC "$PRIMER_MAX_END_GC" config.txt
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293 set_config_value PRIMER_MIN_TM "$PRIMER_MIN_TM" config.txt
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294 set_config_value PRIMER_MAX_TM "$PRIMER_MAX_TM" config.txt
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295 set_config_value PRIMER_OPT_TM "$PRIMER_OPT_TM" config.txt
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296 set_config_value PRIMER_PAIR_MAX_DIFF_TM "$PRIMER_PAIR_MAX_DIFF_TM" config.txt
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297 #
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298 # Run pal_finder
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299 perl $PALFINDER_SCRIPT_DIR/pal_finder_v0.02.04.pl config.txt 2>&1 | tee pal_finder.log
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300 #
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301 # Check that log ends with "Done!!" message
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302 if [ -z "$(tail -n 1 pal_finder.log | grep Done!!)" ] ; then
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303 echo ERROR pal_finder failed to complete successfully >&2
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304 exit 1
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305 fi
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306 #
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307 # Run the pal_finder_filter.pl script from Graeme Fox
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308 if [ ! -z "$FILTERED_MICROSATS" ] ; then
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309 perl $PALFINDER_FILTER_PL Output/PAL_summary.txt 2>&1
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310 if [ $? -ne 0 ] ; then
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311 echo ERROR pal_finder_filter.pl exited with non-zero status >&2
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312 exit 1
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313 elif [ ! -f pal_finder_filter_output.txt ] ; then
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314 echo ERROR no output from pal_finder_filter.pl >&2
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315 exit 1
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316 fi
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317 fi
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318 #
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319 # Clean up
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320 if [ -f Output/microsat_summary.txt ] ; then
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321 /bin/mv Output/microsat_summary.txt $MICROSAT_SUMMARY
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322 fi
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323 if [ -f Output/PAL_summary.txt ] ; then
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324 /bin/mv Output/PAL_summary.txt $PAL_SUMMARY
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325 fi
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326 if [ ! -z "$FILTERED_MICROSATS" ] && [ -f pal_finder_filter_output.txt ] ; then
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327 echo Moving pal_finder_filter_output.txt to $FILTERED_MICROSATS
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328 /bin/mv pal_finder_filter_output.txt $FILTERED_MICROSATS
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329 fi
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330 if [ ! -z "$OUTPUT_CONFIG_FILE" ] && [ -f config.txt ] ; then
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331 /bin/mv config.txt $OUTPUT_CONFIG_FILE
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332 fi
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333 ##
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334 #
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