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1 #!/usr/bin/env bash
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2 DIR=$1
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3 COV=$2
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4 SIM=$3
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5 THR=$4
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6 EXT=$5
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7 OUT=$6
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8
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9
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10 BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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11
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12 array=()
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13 x=0
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14
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15 echo "WARNING: FULL COMPARISON IS ENABLED"
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16
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17 if [ $# != 6 ]; then
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18 echo "***ERROR*** Use: $0 metagenomes_directory coverage similarity threads file_extension outpath"
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19 exit -1
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20 fi
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21
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22 for elem in $(ls -d $DIR/*.$EXT | awk -F "/" '{print $NF}' | awk -F ".$EXT" '{print $1}')
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23 do
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24 array[$x]=$elem
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25 x=`expr $x + 1`
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26 #echo "X: $elem"
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27 done
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28
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29 for ((i=0 ; i < ${#array[@]} ; i++))
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30 do
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31 for ((j=i ; j < ${#array[@]} ; j++))
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32 do
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33 if [ $i != $j ]; then
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34 seqX=${array[$i]}
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35 seqY=${array[$j]}
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36 #echo "----------${seqX}-${seqY}-----------"
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37 if [[ ! -f $6/${seqX}-${seqY}.align ]]; then #if the file does not exist
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38
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39
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40 ${BINDIR}/IMSAME -query $DIR/${seqX}.$EXT -db $DIR/${seqY}.$EXT -n_threads $THR --full -coverage $COV -identity $SIM -out $6/${seqX}-${seqY}.align
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41 grep "(" $6/${seqX}-${seqY}.align | awk '{print $4, $5, $6}' | sed 's/%//g' > $6/${seqX}-${seqY}.align.filtered
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42
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43 ${BINDIR}/covident $6/${seqX}-${seqY}.align.filtered $6/${seqX}-${seqY}.align.filtered.mat
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44
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45 fi
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46
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47
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48
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49
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50
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51 if [[ ! -f $6/${seqX}-${seqY}.r.align ]]; then #if the reversed alignment does not exist
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52 # Compute reverse complement
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53 ${BINDIR}/revComp $DIR/${seqY}.$EXT $DIR/${seqY}.r.${EXT}
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54 ${BINDIR}/IMSAME -query $DIR/${seqX}.$EXT -db $DIR/${seqY}.r.$EXT -n_threads $THR --full -coverage $COV -identity $SIM -out $6/${seqX}-${seqY}.r.align
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55 grep "(" $6/${seqX}-${seqY}.r.align | awk '{print $4, $5, $6}' | sed 's/%//g' > $6/${seqX}-${seqY}.r.align.filtered
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56
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57 ${BINDIR}/covident $6/${seqX}-${seqY}.r.align.filtered $6/${seqX}-${seqY}.align.filtered.mat
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58
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59 fi
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60
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61
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62
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63 fi
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64 rm $DIR/${seqY}.r.${EXT}
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65 done
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66
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67 done
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