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annotate gbsx_digest.sh @ 22:062399f3787f draft

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new version of gbsx: v1.2 with barcodeGenerator, demultiplex and digest
author koen
date Tue, 26 Jan 2016 07:38:36 -0500
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1 #!/usr/bin/env bash
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2
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3 #export PATH=$PATH:$(dirname $0)
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4 #BASEDIR=$(dirname $0)
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5
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6
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7 genome=$1
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8 length=$2
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9 enzyme_combination=$3
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10 dualEnzyme="0"
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11 min_size=$4
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12 max_size=$5
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13 digest_bed=$6
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14 digest_result=$7
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15
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16 awk 'BEGIN {n_seq=0;} /^>/ {if(n_seq%1==0){file=$1".fa"; sub(">","",file)} print >> file; n_seq++; print file >> "list.txt"; next;} { print >> file; }' < $genome
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17
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18 case "$enzyme_combination" in
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19 ApeKI)
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20 enzyme="ApeKI"
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21 cutsite="G^CWGC"
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22 ;;
062399f3787f new version of gbsx: v1.2 with barcodeGenerator, demultiplex and digest
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23 PstI)
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24 enzyme="PstI"
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25 cutsite="CTGCA^G"
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26 ;;
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27 EcoT22I)
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28 enzyme="EcoT22I"
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29 cutsite="ATGCA^T"
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30 ;;
062399f3787f new version of gbsx: v1.2 with barcodeGenerator, demultiplex and digest
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31 PasI)
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32 enzyme="PasI"
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33 cutsite="CC^CWGGG"
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34 ;;
062399f3787f new version of gbsx: v1.2 with barcodeGenerator, demultiplex and digest
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35 HpaII)
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36 enzyme="HpaII"
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37 cutsite="C^CGG"
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38 ;;
062399f3787f new version of gbsx: v1.2 with barcodeGenerator, demultiplex and digest
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39 MspI)
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40 enzyme="MspI"
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41 cutsite="C^CGG"
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42 ;;
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43 PstI-EcoT22I)
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44 dualEnzyme="1"
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45 enzyme="PstI"
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46 cutsite="CTGCA^G"
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47 enzyme2="EcoT22I"
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48 cutsite2="ATGCA^T";
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49 ;;
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50 PstI-MspI)
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51 dualEnzyme="1"
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52 enzyme="PstI"
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53 cutsite="CTGCA^G"
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54 enzyme2="MspI"
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55 cutsite2="C^CGG"
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56 ;;
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57 PstI-TaqI)
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58 dualEnzyme="1"
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59 enzyme="PstI"
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60 cutsite="CTGCA^G"
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61 enzyme2="TaqI"
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62 cutsite2="T^CGA"
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63 ;;
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64 SbfI-MspI)
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65 dualEnzyme="1"
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66 enzyme="SbfI"
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67 cutsite="CCTGCA^GG"
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68 enzyme2="MspI"
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69 cutsite2="C^CGG"
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70 ;;
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71 AsiSI-MspI)
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72 dualEnzyme="1"
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73 enzyme="AsiSI"
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74 cutsite="GCCGAT^CGC"
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75 enzyme2="MspI"
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76 cutsite2="C^CGG"
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77 ;;
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78 BssHII-MspI)
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79 dualEnzyme="1"
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80 enzyme="BssHII"
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81 cutsite="G^CGCGC"
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82 enzyme2="MspI"
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83 cutsite2="C^CGG"
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84 ;;
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85 FseI-MspI)
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86 dualEnzyme="1"
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87 enzyme="FseI"
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88 cutsite="GGCCGG^CC"
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89 enzyme2="MspI"
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90 cutsite2="C^CGG"
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91 ;;
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92 SalI-MspI)
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93 dualEnzyme="1"
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94 enzyme="SalI"
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95 cutsite="G^TCGAC"
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96 enzyme2="MspI"
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97 cutsite2="C^CGG"
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98 ;;
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99 ApoI)
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100 enzyme="ApoI"
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101 cutsite="R^AATTY"
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102 ;;
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103 BamHI)
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104 enzyme="BamHI"
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105 cutsite="G^GATCC"
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106 ;;
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107 MseI)
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108 enzyme="MseI"
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109 cutsite="T^TAA"
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110 ;;
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111 Sau3AI)
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112 enzyme="Sau3AI"
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113 cutsite="^GATC"
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114 ;;
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115 RBSTA)
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116 enzyme="RBSTA"
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117 cutsite="^TA"
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118 ;;
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119 RBSCG)
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120 enzyme="RBSCG"
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121 cutsite="^CG"
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122 ;;
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123 NspI)
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124 enzyme="NspI"
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125 cutsite="RCATG^Y"
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126 ;;
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127 AvaII)
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128 enzyme="AvaII"
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129 cutsite="G^GWCC"
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130 ;;
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131 esac
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132
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133 extraparameters="";
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134 if [ "$dualEnzyme" != "0" ];
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135 then
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136 extraparameters="-E $enzyme2 -D $cutsite2";
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137 fi
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138
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139 perl $GBSX_PATH/GBSX_digest.pl -f list.txt -l $length -d $cutsite -e $enzyme $extraparameters -n $min_size -m $max_size;
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140
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141 rm *.fa;
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142 rm list.txt;
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143
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144 if [ "$dualEnzyme" != "0" ];
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145 then
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146 cat "genome."$enzyme"."$enzyme2"."$length"nt.digest.bed" > $digest_bed;
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147 cat "genome."$enzyme"."$enzyme2"."$length"nt.digest_results" > $digest_result;
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148 else
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149 cat "genome."$enzyme"."$length"nt.digest.bed" > $digest_bed;
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150 cat "genome."$enzyme"."$length"nt.digest_results" > $digest_result;
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151 fi
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152
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153