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1 #!/usr/bin/env bash
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2 DIR=$1
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3 DIR2=$2
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4 EXT=$3
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5 DIM=$4
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6 KMER=$5
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7
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8
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9
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10 if [ $# != 5 ]; then
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11 echo "***ERROR*** Use: $0 genomesDirectory1 genomesDirectory2 extension dim kmer"
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12 exit -1
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13 fi
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14
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15 indexnameA=$(basename "$DIR")
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16 indexnameB=$(basename "$DIR2")
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17
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18 BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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19
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20
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21 array=()
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22 x=0
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23 array2=()
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24
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25 for elem in $(ls -d $DIR/*.$EXT | awk -F "/" '{print $NF}' | awk -F ".$EXT" '{print $1}')
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26 do
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27 array[$x]=$elem
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28 x=`expr $x + 1`
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29 #echo "X: $elem"
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30 done
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31
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32 x=0
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33
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34 for elem in $(ls -d $DIR2/*.$EXT | awk -F "/" '{print $NF}' | awk -F ".$EXT" '{print $1}')
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35 do
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36 array2[$x]=$elem
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37 x=`expr $x + 1`
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38 #echo "X: $elem"
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39 done
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40
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41 for ((i=0 ; i < ${#array[@]} ; i++))
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42 do
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43 for ((j=0 ; j < ${#array2[@]} ; j++))
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44 do
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45 seqX=${array[$i]}
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46 seqY=${array2[$j]}
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47 echo "----------${seqX}-${seqY}-----------"
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48
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49
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50 #echo "$BINDIR/run_and_plot_chromeister.sh $DIR/${seqX}.$EXT $DIR/${seqY}.$EXT 30 10000"
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51 if [[ ! -f ${seqX}.$EXT-${seqY}.$EXT.mat ]]; then
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52 $BINDIR/run_and_plot_chromeister.sh $DIR/${seqX}.$EXT $DIR2/${seqY}.$EXT $KMER $DIM
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53 fi
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54
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55 done
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56 done
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57
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58
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59 # generate index
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60 if [[ ! -f index.csv.temp ]] && [ ! -f index-$indexnameA-$indexnameB.csv ]; then
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61
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62 echo "Launching... $BINDIR/index_chromeister_solo.sh . index-$indexnameA-$indexnameB.csv $DIR $DIR2"
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63 $BINDIR/index_chromeister_solo.sh . index-$indexnameA-$indexnameB.csv $DIR $DIR2
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64 fi
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65
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66
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67
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