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1 #!/bin/bash
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2
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3 while getopts "f:t:o:g:n:r:" optionName; do
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4 case "$optionName" in
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5
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6 f) inputfile="$OPTARG";;
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7 t) minHeight="$OPTARG";;
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8 o) output="$OPTARG";;
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9 g) BUILD="$OPTARG";;
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10 n) nameBed="$OPTARG";;
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11 r) ROOT_DIR="$OPTARG";;
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12 esac
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13 done
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14
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15 local_path=/usr/bin/peakstobed
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16 DATABASE_PATH=$ROOT_DIR/database/files
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17 mkdir -p $DATABASE_PATH/nebulaAnnotations
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18 mkdir -p $DATABASE_PATH/nebulaAnnotations/$BUILD
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19 nebulaAnnotationPath=$DATABASE_PATH/nebulaAnnotations
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20 nebulaGenomePath=$DATABASE_PATH/nebulaAnnotations/$BUILD
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21
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22 ############### Create annotations files ################
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23
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24 FAIFILE='n'
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25 LENFILE='n'
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26 DICTFILE='n'
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27 CHROFILE='n'
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28 MAPFILE='n'
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29
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30 if [ ! -f $nebulaGenomePath/$BUILD.len ]; then
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31 FAIFILE='y'
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32 LENFILE='y'
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33 fi
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34
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35 chrom_info_file=$nebulaGenomePath/$BUILD.len
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36 FILEPATH=$ROOT_DIR/tool-data
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37
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38 bash /usr/bin/create_annotation_files.sh $FAIFILE $LENFILE $DICTFILE $CHROFILE $FILEPATH $BUILD $MAPFILE $nebulaGenomePath
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39
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40 #################### END ANNOTATION FILES ###########################
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41
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42 perl $local_path/peaks2bed.pl -f $inputfile -t $minHeight -o $output -g $chrom_info_file -n $nameBed
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43
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