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view IMSAME/bin/all_vs_all_metagenomes_IMSAME.sh @ 5:353e5673bcb8 draft default tip
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author | bitlab |
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date | Mon, 17 Dec 2018 12:20:41 -0500 |
parents | 762009a91895 |
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#!/usr/bin/env bash DIR=$1 COV=$2 SIM=$3 THR=$4 EXT=$5 OUT=$6 BINDIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" array=() x=0 echo "WARNING: FULL COMPARISON IS ENABLED" if [ $# != 6 ]; then echo "***ERROR*** Use: $0 metagenomes_directory coverage similarity threads file_extension outpath" exit -1 fi for elem in $(ls -d $DIR/*.$EXT | awk -F "/" '{print $NF}' | awk -F ".$EXT" '{print $1}') do array[$x]=$elem x=`expr $x + 1` #echo "X: $elem" done for ((i=0 ; i < ${#array[@]} ; i++)) do for ((j=i ; j < ${#array[@]} ; j++)) do if [ $i != $j ]; then seqX=${array[$i]} seqY=${array[$j]} #echo "----------${seqX}-${seqY}-----------" if [[ ! -f $6/${seqX}-${seqY}.align ]]; then #if the file does not exist ${BINDIR}/IMSAME -query $DIR/${seqX}.$EXT -db $DIR/${seqY}.$EXT -n_threads $THR --full -coverage $COV -identity $SIM -out $6/${seqX}-${seqY}.align grep "(" $6/${seqX}-${seqY}.align | awk '{print $4, $5, $6}' | sed 's/%//g' > $6/${seqX}-${seqY}.align.filtered ${BINDIR}/covident $6/${seqX}-${seqY}.align.filtered $6/${seqX}-${seqY}.align.filtered.mat fi if [[ ! -f $6/${seqX}-${seqY}.r.align ]]; then #if the reversed alignment does not exist # Compute reverse complement ${BINDIR}/revComp $DIR/${seqY}.$EXT $DIR/${seqY}.r.${EXT} ${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 grep "(" $6/${seqX}-${seqY}.r.align | awk '{print $4, $5, $6}' | sed 's/%//g' > $6/${seqX}-${seqY}.r.align.filtered ${BINDIR}/covident $6/${seqX}-${seqY}.r.align.filtered $6/${seqX}-${seqY}.align.filtered.mat fi fi rm $DIR/${seqY}.r.${EXT} done done