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1 #!/usr/bin/env bash
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2 DIR=$1
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3 FASTAS1=$3
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4 FASTAS2=$4
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5 OUT=$2
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6
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7 echo "Computing index CSV..." > index.csv.temp
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8
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9 while [ "$(find . -size 0 | wc -l)" -ne 0 ]; do
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10 sleep 10s
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11 done
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12
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13
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14 EXT="mat"
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15 EXTSCORE="scr.txt"
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16 EXTGENERAL=".fa.fasta"
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17
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18
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19
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20 if [ $# != 4 ]; then
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21 echo "***ERROR*** Use: $0 <directory> <out> <fastas_directory_1> <fastas_directory_2>"
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22 exit -1
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23 fi
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24
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25 rm $DIR/*.log
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26
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27 for i in $DIR/*.scr; do mv $i $i.txt; done
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28
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29 rm $OUT
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30
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31 for elem in $(ls -d $DIR/*.$EXT | awk -F "/" '{print $NF}' | awk -F ".$EXT" '{print $1}')
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32 do
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33 IFS='-', read -a splits <<< "$elem"
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34 IFS='.', read -a getnum <<< "$elem"
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35
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36 scorepath=$(basename $elem .mat).$EXTSCORE
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37
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38 sed -i "/X.*/d" $DIR/$scorepath
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39 sed -i "s/\[1\]//g" $DIR/$scorepath
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40
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41 score=$( head -1 $DIR/$scorepath)
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42
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43 file1=${splits[0]}
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44 file2=$(basename ${splits[1]} .mat)
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45
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46 ID1=$(head -1 $FASTAS1/$file1)
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47 ID2=$(head -1 $FASTAS2/$file2)
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48
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49
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50 #scorepath="$(basename $elem .mat).$EXTSCORE"
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51 #score="$(head -1 $DIR/$scorepath)"
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52
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53 counter=0
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54 numX=0
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55 numY=0
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56 for i in "${getnum[@]}"
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57 do
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58 counter=`expr $counter + 1`
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59 if [ "$numX" -eq 0 ] && [ "$i" == "chromosome" ]; then
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60 numX=$counter
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61 continue
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62 fi
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63 if [ "$numX" -ne 0 ] && [ "$i" == "chromosome" ]; then
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64 numY=$counter
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65 fi
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66
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67 done
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68
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69
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70 echo "$(basename ${splits[0]} $EXTGENERAL),$(basename ${splits[1]} ${EXTGENERAL}.mat),$ID1,$ID2,$elem.$EXT.filt.png,${getnum[${numX}]},${getnum[${numY}]},$score" >> $OUT
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71
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72 done
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73
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74 sort -k5,5n -k6,6n -o $OUT $OUT
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75
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76
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77 sed -i '1iSpX, SpY, IDX, IDY, IMG, CHNumberX, CHNumberY, Score' $OUT
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78
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79 rm index.csv.temp
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80
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