83 lines
2.8 KiB
Bash
83 lines
2.8 KiB
Bash
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#!/bin/bash
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#
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# BUILD THE COORIENTATION GRAPH
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#
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# From a set of sequences, this commande build a graph where:
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# - vertices are sequence id
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# - relation is : s oriented in the same way
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#
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# The same ortientation is defined from the similiarity measured by blast
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# The result graph is formated following the tgf format (trivial graph format)
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# NODE1 NODE2 EDGE_LABEL
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#
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# Run the command
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#
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# coorienteSC.sh <FASTA_FILE> <MINLENGTH> [LOGFILE]
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#
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# <FASTA_FILE> : the fasta file containing sequences to analyse
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# <MINLENGTH> : the cumulative minimum length strand have to share to conclude
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# <LOGFILE> : an optional logfile name
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#
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#========================================================================================
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# -- CAUTION -- Works as long than the script
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# is not called through a symlink
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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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pushTmpDir ORG.coorienteSC
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if [[ ! -z $3 ]]; then
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openLogFile $3
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fi
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DATA="${CALL_DIR}/${1}"
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MINLENGTH=$2
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BLASTDB=${1/.fasta$/}
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loginfo "Build temporary blast DB..."
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makeblastdb -in "${DATA}" -dbtype nucl -out "${BLASTDB}" >& /dev/null
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loginfo "Done"
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loginfo "Running Blast..."
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blastn -db "${BLASTDB}" -query "${DATA}" -outfmt 6 | \
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awk ' \
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($4 > 1000) && ($3 > 70) \
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($1==QUERY) && \
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($2==SUBJECT) && \
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(($7<$8) && ($9<$10)) || (($7>$8) && ($9>$10)) {LSAME+= ($3/100.*$4)} \
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($4 > 1000) && ($3 > 70) \
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($1==QUERY) && \
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($2==SUBJECT) && \
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(($7<$8) && ($9>$10)) || (($7>$8) && ($9<$10)) {LDIFF+= ($3/100.*$4)} \
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(QUERY!="") && \
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(($1!=QUERY) || ($2!=SUBJECT)) {print QUERY,SUBJECT,LSAME,LDIFF,(LSAME>LDIFF)} \
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(($1!=QUERY) || ($2!=SUBJECT)) {QUERY=$1;SUBJECT=$2; \
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LSAME=0; \
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LDIFF=0; \
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if (($4 > 1000) && ($3 > 70)) { \
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if ((($7<$8) && ($9<$10)) || \
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(($7>$8) && ($9>$10))) {\
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LSAME= ($3/100.*$4) } \
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else { \
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LDIFF= ($3/100.*$4) }} \
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} \
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END {print QUERY,SUBJECT,LSAME,LDIFF,(LSAME>LDIFF)}' | \
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awk -v minlength="${MINLENGTH}" \
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' (($3>minlength) || \
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($4 > minlength)) && \
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($3/($4+1) > 2) && \
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($1!=$2) { if ($1 > $2) \
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{ print $2,$1,$5 } \
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else \
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{print $1,$2,$5}}' | \
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sort | \
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uniq -c | \
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awk '($1==2) {print $2,$3,$4}'
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loginfo "Done"
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popTmpDir
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