Eric Coissac
d4da1d01fd
clusterizecore.sh script from the detectors/cds/lib folder. The CDS detector is now modified to use the clean.fst files. Former-commit-id: e30a53b5b6b658388af4b2640b30e6765c729894 Former-commit-id: 3015ad50d25248fb117ab00e816b00fde1f9ba1d
91 lines
1.8 KiB
Bash
Executable File
91 lines
1.8 KiB
Bash
Executable File
#!/bin/bash
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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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CORELIB="${CDS_DATA_DIR}/chlorodb/core"
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CDHIT_ID=0.7
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CDHIT_DELTA=0.8
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function clusterize() {
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local prot="${1}"
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local fastain="${prot}.fst"
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local cdhitout="${prot}.cdhit"
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local fasta1="${prot}.1l.fst"
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rm -rf "${prot}"
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mkdir -p "${prot}"
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cd-hit -i "${fastain}" \
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-o "${prot}/${cdhitout}" \
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-c ${CDHIT_DELTA} \
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-G 1 \
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-g 1 \
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-aL 0.95 \
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-s ${CDHIT_ID} \
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-b 350 -p 1 \
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-d 0 -n 3
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fasta1line "${fastain}" > "${prot}/${fasta1}"
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pushd "$prot"
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rm -rf "*.cluster.*.ids"
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$AwkCmd -v prot="$prot" \
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'/^>/ {cluster=$2} \
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! /^>/ {sub("\\.\\.*$","",$3); \
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filename=prot".cluster."cluster".ids"; \
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print $3 >> filename ; \
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close(filename) }' "${cdhitout}.clstr"
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rm -f "../$prot.clean.fst"
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for ids in *.cluster.*.ids ; do
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cluster=$(printf "%03d" $(echo "${ids}" | $AwkCmd -F'.' '{print $3}'))
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size=$(wc -l "$ids" | $AwkCmd '{print $1}')
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fsize=$(printf '%05d' $size)
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alignment="${prot}.cluster.${fsize}.${cluster}.fst"
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if (( size > 1 )) ; then
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egrep -f "$ids" -A 1 "${fasta1}" | \
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egrep -v -- '^--$' | \
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clustalo -i - > "$alignment"
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else
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egrep -f "$ids" -A 1 "${fasta1}" | \
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egrep -v -- '^--$' > "$alignment"
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fi
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if (( size >= 5 )) ; then
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egrep -f "$ids" -A 1 "${fasta1}" | \
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egrep -v -- '^--$' | \
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formatfasta >> "../$prot.clean.fst"
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fi
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rm -f "$ids"
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done
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rm -f "${fasta1}"
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rm -f "${cdhitout}"
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popd
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}
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pushd $CORELIB
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rm -rf *.clean.fst
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for prot in *.fst ; do
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prot="${prot/.fst/}"
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clusterize "$prot"
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done
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popd |