Eric Coissac
ee634cc779
from plastomes where the three categories of CAU tRNA (Met/Ile/fMet) are annotated Former-commit-id: 67dc445698e22fe8a503c6700977c79e4817d302 Former-commit-id: 6e84303543b0752a7946bdde6e5114cfe6eef8da
73 lines
2.7 KiB
Bash
Executable File
73 lines
2.7 KiB
Bash
Executable File
#!/bin/bash
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#
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# BUILD REFERENCE THE CAU TRNA 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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function fasta1li {
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$AwkCmd '/^>/ {if (sequence) \
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{print sequence}; \
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print $0; \
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sequence=""} \
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!/^>/ {sequence = sequence $0} \
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END {print sequence}' $1
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}
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function filtertrna() {
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$AwkCmd -F '_' 'BEGIN {RS=">"} \
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(! /^$/) {trna=$1; \
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ac=$2"_"$3;} \
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(ac!=oldac && \
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trnas["trnfM"]==1 && \
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trnas["trnM"]==1 && \
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trnas["trnI"]==1 \
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) {print seqs} \
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(ac!=oldac) {trnas["trnfM"]=0; \
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trnas["trnM"]=0; \
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trnas["trnI"]=0; \
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seqs=""; \
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oldac=ac \
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} \
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(! /^$/) {seqs=seqs"\n>"$0; \
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trnas[trna]=1;} \
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END {if (trnas["trnfM"]==1 && \
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trnas["trnM"]==1 && \
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trnas["trnI"]==1) \
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print seqs}' $1 | \
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egrep -v "^ *$"
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}
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pushTmpDir ORG.buildSCDB
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CAUFILE=CAU.fasta
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openLogFile "${TRNA_DATA_DIR}/CAU_tRNA_DB.log"
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loginfo "Selecting Viridiplantae genebank entries..."
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VIRIDIPLANTAE=$(${PROG_DIR}/../../normalize/tools/selectViridiplantae.sh $*)
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loginfo " --> $(echo ${VIRIDIPLANTAE} | wc -w) entries selected"
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loginfo "Done"
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loginfo "Extracting the CAU tRNA from the plants entries..."
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${PROG_DIR}/extract_refCAUtRNA.sh ${VIRIDIPLANTAE} | \
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fasta1li | \
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egrep -A 1 '^>trn(I|M|fM)' | \
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grep -v -- -- | \
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filtertrna > ${CAUFILE}
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loginfo "Done"
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loginfo "Installing the CAU tRNA database..."
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cp ${CAUFILE} "${TRNA_DATA_DIR}/CAU_tRNA_DB.fasta"
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loginfo "Done"
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popTmpDir |