107 lines
3.4 KiB
Bash
107 lines
3.4 KiB
Bash
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#!/bin/bash
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#
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# BUILD REFERENCE : THE RPS12 LIBRARY
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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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THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${THIS_DIR}/../../../scripts/bash_init.sh"
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source "${THIS_DIR}/lib/clusterize_prot.sh"
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function extract_rps12() {
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$AwkCmd ' \
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/^LOCUS/ {LOCUS=$2;} \
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/^ [^ ]/ { if (CDS) { \
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print LOCUS "/" feature; \
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print "#################" \
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} \
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CDS=0; \
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} \
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/^ CDS / {CDS=1; \
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$1=""; \
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feature=""} \
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(CDS) { sub(/^ */,"",$0); \
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sub(/ *$/,"",$0); \
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feature=feature $0} \
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' \
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| egrep -i '"rps12"' \
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| $AwkCmd -F"/" ' \
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function printfasta(seq) { \
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seqlen=length(seq); \
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for (i=1; i <= seqlen; i+=60) \
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print substr(seq,i,60); \
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} \
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\
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($1 != current) {current=$1; \
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n=1 \
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} \
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{$1=$1 "_rps12_" n; \
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n++; \
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delete keys; \
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for (i=3; i<=NF; i++) { \
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split($i,key,"="); \
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keys[key[1]]=key[2] \
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} \
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prot = keys["translation"]; \
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gsub(/"/,"",prot); \
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print ">" $1,"location=" $2 ";"; \
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printfasta(prot) \
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} \
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'
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}
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pushTmpDir ORG.buildRPS12DB
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RPS12FILE=RPS12_prot.fst
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openLogFile "${CDS_DATA_DIR}/chlorodb/RPS12_DB.log"
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loginfo "Selecting Viridiplantae genbank entries..."
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VIRIDIPLANTAE=$(${PROG_DIR}/../../normalize/tools/selectViridiplantae.sh $*)
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loginfo " --> $(echo ${VIRIDIPLANTAE} | wc -w) entries selected"
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loginfo "Done"
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loginfo "Extracting the RPS12 protein sequences from the plants entries..."
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( for gbk in ${VIRIDIPLANTAE} ; do
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gzcat $gbk | \
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extract_rps12
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done ) > ${RPS12FILE}
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loginfo "Done"
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loginfo "Installing the RPS12 protein sequence database..."
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cp ${RPS12FILE} "${CDS_DATA_DIR}/chlorodb/RPS12_DB.fst"
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loginfo "Done"
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popTmpDir
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pushd "${CDS_DATA_DIR}/chlorodb"
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loginfo "Clusterizing the RPS12 protein sequence database..."
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rm -rf RPS12_DB.clean.fst
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clusterize RPS12_DB
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loginfo "Done"
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loginfo " formatting Blast RPS12 DB"
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timeoutcmd 300 makeblastdb -dbtype prot -in RPS12_DB.clean.fst >& /dev/null
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loginfo "Done"
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popd
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#
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# format blast protein database
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#
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loginfo "Done"
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