4b71fe8c4c
modified: .gitignore new file: data/cds/sp_chlorodb/parameters.sh deleted: data/ir/LSC_RefDB.fasta deleted: data/ir/SSC_RefDB.fasta modified: detectors/cds/bin/go_cds.sh modified: detectors/normalize/lib/lookforIR.lib.sh modified: detectors/normalize/lib/selectIR.py modified: organnot/Dockerfile new file: organnot/README.md new file: organnot/dorgannot deleted: ports/.DS_Store deleted: src/ncbiblast/binaries/.gitignore deleted: src/prokov/lxpack/tests/S.fasta deleted: src/prokov/lxpack/tests/St.fasta deleted: src/prokov/lxpack/tests/Stt.fasta deleted: src/prokov/lxpack/tests/aS.fasta deleted: src/prokov/lxpack/tests/aSt.fasta deleted: src/prokov/lxpack/tests/aStt.fasta deleted: src/prokov/lxpack/tests/aaS.fasta deleted: src/prokov/lxpack/tests/aaSt.fasta deleted: src/prokov/lxpack/tests/aaStt.fasta new file: src/repseek/repseek-2014.09.tgz
76 lines
2.0 KiB
Bash
76 lines
2.0 KiB
Bash
#!/bin/bash
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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SELECTIR="${PROG_DIR}/../../normalize/lib/selectIR.py"
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function lookForIR {
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local QUERY="$1"
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local MATCHES=$(basename ${QUERY})
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MATCHES="${MATCHES/.*/}.matches"
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local REPEATS="${MATCHES/.*/}.repseek"
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# Blast columns:
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# query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
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# We keep blast matches if :
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# The match is longer than 1000
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# The identity is higher than 80%
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#
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# The match file has the following format:
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# LSC/SSC begin end same_strand=1/diff_strand=0
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loginfo "Locating SSC and LSC by similarity..."
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blastn -db ${SCDB} \
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-query ${QUERY} \
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-outfmt 6 \
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-max_target_seqs 10000 | \
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awk -v id_match=80 -v lmin=100 \
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'($4+0 > lmin) && (($3+0)>id_match) {
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SAME=(($7+0 < $8+0) && ($9+0 < $10+0)) || (($7+0 > $8+0) && ($9+0 > $10+0));
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if ($7+0 < $8+0)
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{print substr($2,1,3),$7,$8,SAME}
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else
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{print substr($2,1,3),$8,$7,SAME}
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}' | \
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sort -nk 2 > ${MATCHES}
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loginfo "Done $(wc -l ${MATCHES} | awk '{print $1}') matches identified"
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loginfo "Looking for long inverted repeats..."
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repseek -c -p 0.001 -i ${QUERY} 2>> /dev/null > ${REPEATS}
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nrepeat="$(wc -l ${REPEATS} | awk '{print $1}')"
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loginfo "Done"
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if (( nrepeat == 0 )) ; then
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logwarning "No inverted repeat identified"
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return 1
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fi
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loginfo " --> ${nrepeat} repeats identified"
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loginfo "Marking and selecting the best inverted repeat..."
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local IR=( $(${SELECTIR} ${MATCHES} ${REPEATS}) )
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loginfo "Done"
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loginfo " --> IR size : IRa = ${IR[5]} / IRb = ${IR[7]}"
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loginfo " --> IR Score: ${IR[8]}"
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deltaIR=$((IR[5] - IR[7]))
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if (( deltaIR < -10 )) || (( deltaIR > 10 )); then
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logwarning "Differences between IR lengths ($deltaIR) is greater than 10"
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fi
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echo "${IR[@]}"
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}
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SCDB="${IR_DATA_DIR}/SC_RefDB"
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if [[ ! "$1" =~ ^/ ]]; then
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QUERY="${CALL_DIR}/$1"
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else
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QUERY="$1"
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fi
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