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18
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1 #!usr/bin/bash
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2
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3 #########################################################################################################
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4 # ARGUMENTS FROM alfa_wrapper.xml #
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5 #########################################################################################################
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6 configFile=$1;
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7 logReport=$2;
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8 sed -i -e '/^$/d; s/\t//g;' $configFile;
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9 printf "__________________________________________________________________\n\n" > $logReport
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10 printf " ALFA CONFIG \n" >> $logReport
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11 printf "__________________________________________________________________\n" >> $logReport
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12 cat $configFile >> $logReport
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13
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14 #########################################################################################################
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15 # INITIALIZATION OF THE VARIABLES from $configFile #
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16 #########################################################################################################
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17 #_INPUT1
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18 annotationSource=`grep -P '^annotationSource ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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19 if [ "$annotationSource" == "personal_gtf" ]; then
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20 annotationFile=`grep -P '^annotationFile ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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21 elif [ "$annotationSource" == "built_in_index" ]; then
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22 built_in_index_prefix=`grep -P '^built_in_index_prefix ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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23 else
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24 strandedIndex=`grep -P '^strandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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25 unstrandedIndex=`grep -P '^unstrandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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26 fi
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27
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28 #_INPUT2
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29 readsType=`grep -P '^readsType ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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30 readsFileList=`grep -P '^readsFile\[[0-9]+\] ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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31 readsLabelList=`grep -P '^readsLabel\[[0-9]+\] ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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32
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33 #_OUTPUT CHOICES
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34 plotChoice=`grep -P '^plotChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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35 countFileChoice=`grep -P '^countFileChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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36 indexChoice=`grep -P '^indexChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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37
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38 #_OUTPUT OPTIONS
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39 strandness=`grep -P '^strandness ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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40 categoriesDepth=`grep -P '^categoriesDepth ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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41 plotFormat=`grep -P '^plotFormat ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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42 plotThresholdChoice=`grep -P '^plotThresholdChoice ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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43 if [ "$plotThresholdChoice" == "True" ]; then
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44 yMin=`grep -P '^yMin ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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45 yMax=`grep -P '^yMax ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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46 fi
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47
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48 #_OUTPUT FILES
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49 if [ "$plotChoice" == "True" ]; then
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50 if [ "$plotFormat" == "pdf" ]; then
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51 outputPdf=`grep -P '^outputPdf ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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52 elif [ "$plotFormat" == "svg" ]; then
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53 outputCategoriesSvg=`grep -P '^outputCategoriesSvg ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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54 outputBiotypesSvg=`grep -P '^outputBiotypesSvg ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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55 else
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56 outputCategoriesPng=`grep -P '^outputCategoriesPng ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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57 outputBiotypesPng=`grep -P '^outputBiotypesPng ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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58 fi
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59 fi
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60 if [ "$countFileChoice" == "True" ]; then
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61 outputCountFile=`grep -P '^outputCountFile ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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62 fi
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63 if [ "$indexChoice" == "True" ]; then
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64 outputStrandedIndex=`grep -P '^outputStrandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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65 outputUnstrandedIndex=`grep -P '^outputUnstrandedIndex ?=' $configFile | awk 'BEGIN{FS="= ?"} {print $2}'`;
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66 fi
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67
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68 #########################################################################################################
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69 # CREATION OF A TMP DIRECTORY FOR THE OUTPUT FILES OF ALFA AND cd #
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70 #########################################################################################################
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71 outputDirectory=`mktemp -d /export/home1/users/biocomp/chbernar/galaxy/database/tmp/tmpXXXXXX`;
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72 if [ -d $outputDirectory ]; then
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73 chmod -R ugo+wrx $outputDirectory;
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74 rm -R $outputDirectory;
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75 fi
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76 mkdir $outputDirectory;
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77 chmod -R ugo+wrx $outputDirectory;
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78 cd $outputDirectory;
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79
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80 #########################################################################################################
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81 # TEST OF INPUT1 #
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82 #########################################################################################################
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83 if [ "$annotationSource" == "index" ]; then
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84 #need to copy the files.dat to .*index because ALFA requires the extension ".(un)stranded.index"
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85 index="index"
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86 cp $strandedIndex $index".stranded.index"
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87 cp $unstrandedIndex $index".unstranded.index"
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88 fi
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89
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90 #########################################################################################################
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91 # TEST OF INPUT2 AND DETERMINATION OF PYTHON READS INPUT ARGUMENT #
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92 #########################################################################################################
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93 readsListLen=`echo "$readsFileList" | wc -l`;
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94 readsInput="";
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95 for (( i = 1; i <= readsListLen; i++ )) do
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96 readsFile[$i]=`echo "$readsFileList" | awk -v i=$i 'NR==i'`;
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97 readsLabel[$i]=`echo "$readsLabelList" | awk -v i=$i 'NR==i' | sed -e 's/ /_/g'`;
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98 if [ "$readsType" == "bam" ]; then
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99 bamSorted=`samtools view -H "${readsFile[$i]}" | grep -c 'SO:unsorted'`
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100 if [ "$bamSorted" != "0" ] ; then
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101 samtools sort ${readsFile[$i]} ${readsFile[$i]}
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102 fi
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103 else
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104 #need to copy the file.dat to tmp.bedgraph because ALFA requires the extension ".bedgraph"
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105 bedgraphFile="tmpBedgraph_"$i
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106 cp ${readsFile[$i]} $bedgraphFile".bedgraph"
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107 readsFile[$i]=$bedgraphFile
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108 fi
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109 if [ "${readsLabel[$i]}" == "" ]; then
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110 readsLabel[$i]="sample_""$i";
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111 fi
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112 readsInput=$readsInput" "${readsFile[$i]}" "${readsLabel[$i]};
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113 done
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114
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115 #########################################################################################################
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116 # DETERMINATION OF THE APPROPRIATE SCRIPTS ARGUMENTS #
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117 #########################################################################################################
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118 scriptPath="/export/home1/users/biocomp/chbernar/galaxy/tools/alfa/";
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119 if [ "$annotationSource" == "index" ]; then
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120 scriptInput="-g $index -i ""$readsInput";
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121 elif [ "$annotationSource" == "built_in_index" ]; then
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122 scriptInput="-g $built_in_index_prefix -i ""$readsInput";
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123 else
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124 scriptInput="-a $annotationFile -i ""$readsInput";
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125 fi
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126 if [ "$readsType" = "bedgraph" ]; then
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127 scriptInput=$scriptInput" --bedgraph";
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128 fi
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129 scriptStrandness="-s "$strandness
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130 scriptCategoriesDepth="-d "$categoriesDepth
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131 if [ "$plotChoice" == "True" ]; then
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132 if [ "$plotFormat" == "pdf" ]; then
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133 scriptPlotOutput="--pdf plotFile.pdf";
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134 else
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135 scriptPlotOutput="--"$plotFormat" plotFile";
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136 fi
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137 if [ "$plotThresholdChoice" == "True" ]; then
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138 scriptPlotOutput=$scriptPlotOutput" -t ""$yMin"" ""$yMax"
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139 fi
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140 else
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141 scriptPlotOutput="--n";
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142 fi
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143
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144 #########################################################################################################
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145 # DISPLAY ALFA PROCESS #
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146 #########################################################################################################
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147 printf "__________________________________________________________________\n\n" >> $logReport
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148 printf " ALFA PROCESS \n" >> $logReport
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149 printf "__________________________________________________________________\n" >> $logReport
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150
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151 if [ "$plotChoice" == "False" ] && [ "$countFileChoice" == "False" ] && [ "$indexChoice" == "False" ]; then
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152 cat <<error 1>&2
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153
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154 No output to return.
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155 Process Aborted
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156 error
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157 exit 0
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158 fi
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159
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160 printf "Command:\n" >> $logReport
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161 echo "python ""$scriptPath"ALFA.py $scriptInput $scriptStrandness $scriptCategoriesDepth $scriptPlotOutput >> $logReport;
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162 printf "\n******************************************************************\n" >> $logReport
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163 printf "Temporary Output Directory:\n" >> $logReport
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164 echo $outputDirectory >> $logReport
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165 printf "\n******************************************************************\n" >> $logReport
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166 printf "ALFA prompt:\n" >> $logReport
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167 python "$scriptPath"ALFA.py $scriptInput $scriptStrandness $scriptCategoriesDepth $scriptPlotOutput >> $logReport 2>errorFile;
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168 printf "\n******************************************************************\n" >> $logReport
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169
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170 #########################################################################################################
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171 # REDIRECTION OF ERRORS - TMP SOURCE ALFA.PY MUST BE CORRECTED SOON #
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172 #########################################################################################################
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173 if [[ -s errorFile ]]; then
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174 #When the option --n is enabled, alfa prints '### End of the program' in stderr even if the process worked-
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175 #The following lines to avoid the tool from crashing in this case
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176 endProgram=`grep -c '### End of program' errorFile`
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177 if [ "$endProgram" == "0" ]; then
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178 #When alfa prints '### End of program' in stdout, all the messages in stderr are considered
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179 #as warnings and not as errors. True errors make the script exits with code "2"
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180 endProgram=`grep -c '### End of program' $logReport`
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181 if [ "$endProgram" == "0" ]; then
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182 >&2 printf "The script ALFA.py encountered the following error:\n\n"
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183 >&2 cat errorFile
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184 printf "ALFA error:\n" >> $logReport
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185 cat errorFile >> $logReport
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186 printf "\n******************************************************************\n" >> $logReport
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187 exit 2
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188 else
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189 >&2 printf "The script ALFA.py encountered the following warning:\n\n"
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190 >&2 cat errorFile
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191 printf "ALFA warning:\n" >> $logReport
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192 cat errorFile >> $logReport
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193 printf "\n******************************************************************\n" >> $logReport
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194 fi
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195 fi
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196 fi
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197
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198 #########################################################################################################
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199 # OUTPUT REDIRECTIONS #
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200 #########################################################################################################
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201 if [ "$plotChoice" == "True" ]; then
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202 if [ "$plotFormat" == "pdf" ]; then
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203 mv "plotFile.pdf" $outputPdf;
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204 elif [ "$plotFormat" == "png" ]; then
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205 mv "plotFile.categories.png" $outputCategoriesPng;
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206 mv "plotFile.biotypes.png" $outputBiotypesPng;
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207 else
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208 mv "plotFile.categories.svg" $outputCategoriesSvg;
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209 mv "plotFile.biotypes.svg" $outputBiotypesSvg;
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210 fi
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211 fi
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212 if [ "$countFileChoice" == "True" ]; then
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213 > countFile;
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214 for (( i = 1; i <= readsListLen; i++ )) do
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215 printf "##LABEL: "${readsLabel[$i]}"\n\n" >> countFile;
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216 cat ${readsLabel[$i]}".categories_counts" >> countFile;
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217 printf "__________________________________________________________________\n" >> countFile;
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218 done
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219 mv countFile $outputCountFile;
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220 fi
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221 if [ "$indexChoice" == "True" ]; then
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222 if [ "$annotationSource" == "index" ]; then
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223 mv $strandedIndex $outputStrandedIndex
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224 mv $unstrandedIndex $outputUnstrandedIndex
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225 elif [ "$annotationSource" == "built_in_index" ]; then
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226 cp $built_in_index_prefix".stranded.index" $outputStrandedIndex
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227 cp $built_in_index_prefix".unstranded.index" $outputUnstrandedIndex
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228 else
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229 annotationFileName=`grep -P -o '[^/]*\.dat$' <<< $annotationFile`
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230 mv $annotationFileName".stranded.index" $outputStrandedIndex
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231 mv $annotationFileName".unstranded.index" $outputUnstrandedIndex
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232 fi
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233 fi |
