Commit dc61a618 by Eric Coissac

First trial to automatcally cleanup the core CDS database

parent 619dc4f5
#!/bin/bash
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
source "${THIS_DIR}/../../../scripts/bash_init.sh"
CORELIB="${CDS_DATA_DIR}/chlorodb/core"
function clusterize() {
local prot="${1}"
local fastain="${prot}.fst"
local cdhitout="${prot}.cdhit"
local fasta1="${prot}.1l.fst"
rm -rf "${prot}"
mkdir -p "${prot}"
cd-hit -i "${fastain}" \
-o "${prot}/${cdhitout}" \
-c 0.6 -G 1 \
-g 1 -s 0.8 \
-b 150 -p 1 \
-d 0 -n 3
fasta1line "${fastain}" > "${prot}/${fasta1}"
pushd "$prot"
rm -rf "*.cluster.*.ids"
$AwkCmd -v prot="$prot" \
'/^>/ {cluster=$2} \
! /^>/ {sub("\\.\\.*$","",$3); \
filename=prot".cluster."cluster".ids"; \
print $3 >> filename ; \
close(filename) }' "${cdhitout}.clstr"
for ids in *.cluster.*.ids ; do
cluster=$(printf "%03d" $(echo "${ids}" | $AwkCmd -F'.' '{print $3}'))
size=$(wc -l "$ids" | $AwkCmd '{print $1}')
fsize=$(printf '%05d' $size)
alignment="${prot}.cluster.${fsize}.${cluster}.fst"
if (( size > 1 )) ; then
egrep -f "$ids" -A 1 "${fasta1}" | \
egrep -v -- '^--$' | \
clustalo -i - > "$alignment"
else
egrep -f "$ids" -A 1 "${fasta1}" | \
egrep -v -- '^--$' > "$alignment"
fi
if (( size >= 10 )) ; then
egrep -f "$ids" -A 1 "${fasta1}" | \
egrep -v -- '^--$' | \
formatfasta >> "$prot.clean.fst"
fi
rm -f "$ids"
done
rm -f "${fasta1}"
rm -f "${cdhitout}"
popd
}
pushd $CORELIB
for prot in *.fst ; do
prot="${prot/.fst/}"
clusterize "$prot"
done
popd
\ No newline at end of file
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