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1 #!/bin/bash
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2
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3
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4 #######################################
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5 # Location specific settings
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6
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7 #scriptsdir="/data/galaxy-dist/tools/trait/circos" # location of tool directory
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8 #confdir=${scriptsdir} # loacation of circos conf files (circos_JSV.conf, circos_JS.conf etc)
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9 #hg18bed="${scriptsdir}/hg18Genes"
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10 #hg19bed="${scriptsdir}/hg19Genes"
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11 #######################################
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12
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13
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14 # arguments <junctions file> <SNParray probes> <SNParray snps> <varfile> <WG file> <montage file> <per_chr_file> <hg18|hg19> <customplotfile> <custom_region> <genetrack> <imageformat>
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15 echo "arguments: $@"
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16
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17
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18 if [ $# -ne 14 ]
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19 then
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20 echo "error, unexpected number of arguments in $0"
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21 exit
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22 fi
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23
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24 junctions=$1
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25 probes=$2
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26 snps=$3
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27 variations=$4
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28 wg_out=$5
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29 montage_out=$6
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30 per_chr_file=$7
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31 build=$8
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32 customplot_file=$9
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33 custom_region=${10//chr/hs}
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34 show_gene_track=${11}
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35 imageformat=${12}
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36 scriptsdir=${13}
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37 confdir=${14}
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38
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39 hg18bed="${scriptsdir}/hg18Genes"
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40 hg19bed="${scriptsdir}/hg19Genes"
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41
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42
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43 # which tracks to show (depending on which files are provided)
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44 if [ $junctions == "None" ]
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45 then
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46 echo "show = no" > show_junctions.txt
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47 else
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48 echo "show = yes" > show_junctions.txt
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49 fi
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50
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51 if [ $variations == "None" ]
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52 then
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53 echo "show = no" > show_variations.txt
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54 else
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55 echo "show = yes" > show_variations.txt
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56 fi
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57
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58 if [ $snps == "None" ]
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59 then
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60 echo "show = no" > show_snps.txt
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61 else
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62 echo "show = yes" > show_snps.txt
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63 fi
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64
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65 if [ $probes == "None" ]
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66 then
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67 echo "show = no" > show_probes.txt
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68 else
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69 echo "show = yes" > show_probes.txt
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70 fi
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71
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72
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73
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74 echo "karyotype = data/karyotype/karyotype.human.hg19.txt" > karyotype.txt
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75 if [ $build == "hg18" ]
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76 then
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77 echo "karyotype = data/karyotype/karyotype.human.hg18.txt" > karyotype.txt
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78 fi
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79
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80 bn=`basename ${junctions}`
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81 junctions_circos="${bn}_J_circos"
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82 probes_circos="${bn}_probes_circos"
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83 snps_circos="${bn}_snps_circos"
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84 variations_circos="${bn}_variations_circos"
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85 variations_circos_chr="${bn}_variations_circos_chr"
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86 bed_junctions="bedfile_junctions_${bn}"
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87 bed_snps="bedfile_snps_${bn}"
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88 impacted_genes="ImpactedGenes.tsv"
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89 circos_out_wg="${bn}_out_wg"
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90 circos_out_montage="${bn}_out_montage"
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91
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92 touch $bed_junctions
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93 touch $bed_snps
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94 touch $impacted_genes
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95
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96
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97
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98 echo ""
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99 echo "galaxy:runCircos.sh: "
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100 echo "junctions $junctions, probes: $probes, snps: $snps, variations: $variations, wg_out: $wgout, montage_out: $montage_out, per_chr_file: $per_chr_file"
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101 echo ""
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102
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103 ## conf file
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104 conffile=${confdir}/circos_JSV.conf
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105
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106
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107
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108 #####################################
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109 #
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110 # input file conversions
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111 #
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112 #####################################
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113
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114
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115 echo "show = ${show_gene_track}" > showgenes.txt
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116
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117 if [ $junctions != "None" ]
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118 then
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119 echo "junctions file specified"
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120 if [[ ! -f $junctions_circos ]]
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121 then
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122 ${scriptsdir}/junctions2circos.sh $junctions $junctions_circos $bed_junctions
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123 fi
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124
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125 if [ ${show_gene_track} == "yes" ]
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126 then
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127
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128 #cat $bed_junctions $bed_snps > ImpactedGenes.tmp
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129 mv $bed_junctions ImpactedGenes.tmp
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130
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131 if [ $build == "hg18" ]
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132 then
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133 intersectBed -a ImpactedGenes.tmp -b $hg18bed -wb > ImpactedGenes.tmp2
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134 else
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135 intersectBed -a ImpactedGenes.tmp -b $hg19bed -wb > ImpactedGenes.tmp2
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136 fi
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137
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138 #generate text-track input file
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139 awk 'BEGIN{
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140 FS="\t"
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141 OFS=" "
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142 }{
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143 print $1,$11,$12,$19
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144 }END{
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145
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146 }' ImpactedGenes.tmp2 > ImpactedGenes.tmp3
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147
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148 sed -i 's/chr/hs/g' ImpactedGenes.tmp3
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149 sort -k4 ImpactedGenes.tmp3 > ImpactedGenes.tmp4
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150 uniq -u -f 3 ImpactedGenes.tmp4 ImpactedGenes.tsv
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151 cat ImpactedGenes.tsv
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152 fi
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153
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154 fi
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155
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156 if [[ $probes != "None" && $snps != "None" ]]
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157 then
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158 echo "probes and snps files specified"
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159
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160 ${scriptsdir}/SNParray2circos.sh $probes $snps $probes_circos $snps_circos
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161
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162 #if too many points, reduce (max 25000)
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163 numpoints=`wc -l $probes_circos |cut -d" " -f1 `
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164 echo "numpoints probes.txt: $numpoints"
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165 while [ $numpoints -gt 25000 ]
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166 do
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167 echo "reducing number of datapoints in probes file"
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168 awk 'BEGIN{
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169 FS="\t"
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170 OFS="\t"
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171 }{
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172 if(FNR%2==1)
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173 print $0 #print alternating lines
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174
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175 }END{}' $probes_circos > probes_circos_reduced
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176
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177 rm $probes_circos
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178 mv probes_circos_reduced $probes_circos
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179 numpoints=`wc -l $probes_circos |cut -d" " -f1 `
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180 done
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181
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182 #if too many points, reduce (max 25000)
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183 numpoints=`wc -l $snps_circos | cut -d" " -f1 `
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184 echo "numpoints snps.txt: $numpoints"
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185 while [ $numpoints -gt 25000 ]
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186 do
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187 echo "reducing number of datapoints in snps file"
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188 awk 'BEGIN{
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189 FS="\t"
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190 OFS="\t"
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191 }{
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192 if(FNR%2==1)
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193 print $0
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194
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195 }END{}' $snps_circos > snps_circos_reduced
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196
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197 rm $snps_circos
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198 mv snps_circos_reduced $snps_circos
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199 numpoints=`wc -l $snps_circos |cut -d" " -f1 `
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200 done
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201
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202
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203 fi
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204
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205
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206 if [ $variations != "None" ]
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207 then
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208 echo "variations file specified"
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209 if [[ ! -f $variations_circos ]]
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210 then
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211 ${scriptsdir}/variations2circos.sh $variations $variations_circos $variations_circos_chr $bed_snps
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212 echo "variations_circos"
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213 cat $variations_circos
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214 fi
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215 fi
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216
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217
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218
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219
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220
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221 #####################################
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222 #
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223 # run circos
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224 #
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225 #####################################
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226
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227
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228 echo "running circos"
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229 ${scriptsdir}/runcircos_JSV.sh ${conffile_JSV} ${junctions_circos} ${probes_circos} ${snps_circos} $wg_out $montage_out $per_chr_file $build ${variations_circos} ${variations_circos_chr} $customplot_file $custom_region $imageformat
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