Eric Coissac
c32f7cdde6
Former-commit-id: f2a75cf99b24875c90c426c2afb22a75b972bf60 Former-commit-id: 65e3dfb35df06ca69bb29b690c9a40e8940ac6bf
177 lines
4.8 KiB
Bash
Executable File
177 lines
4.8 KiB
Bash
Executable File
#!/bin/bash
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#
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# BUILD REFERENCE SINGLE COPY LIBRARIES
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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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SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
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source "${SCRIPT_DIR}/../../../scripts/bash_init.sh"
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pushTmpDir ORG.buildSCDB
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openLogFile "${IR_DATA_DIR}/SingleCopyDB.log"
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loginfo "Selecting Viridiplantae genebank entries..."
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VIRIDIPLANTAE=$(${PROG_DIR}/selectViridiplantae.sh $*)
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loginfo " --> $(echo ${VIRIDIPLANTAE} | wc -w) entries selected"
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loginfo "Done"
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#
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# Deals with Long Single Copies (LSC)
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#
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loginfo "Extracting Long Single Copies (LSC)..."
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${PROG_DIR}/extract_refLSC.sh ${VIRIDIPLANTAE} > LSC.fasta
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loginfo " --> $(fastaCount LSC.fasta) retreived sequences"
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loginfo "Done"
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loginfo "Building LSC coorientation graph..."
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${PROG_DIR}/coorienteSC.sh LSC.fasta 20000 ${ORG_LOGFILE} > LSC.tgf
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${PROG_DIR}/cc.py LSC.tgf > LSC.cc
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loginfo " --> $(awk '{print $1}' LSC.cc | uniq | wc -l) connected componants"
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loginfo "Done"
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loginfo "Indexing LCS..."
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fastaindex -f LSC.fasta -i LSC.index
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loginfo "Done"
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loginfo "Extracting main connected components for LCS..."
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rm -f LSC.direct.fasta
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touch LSC.direct.fasta
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for id in `awk '($1==0) {print $2}' LSC.cc`; do
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fastafetch -f LSC.fasta -i LSC.index -q "${id}" >> LSC.direct.fasta
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done
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loginfo " --> $(fastaCount LSC.direct.fasta) sequences"
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loginfo "Done"
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loginfo "Extracting second connected components for LCS..."
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rm -f LSC.reverse.fasta
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touch LSC.reverse.fasta
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for id in `awk '($1==1) {print $2}' LSC.cc`; do
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fastafetch -f LSC.fasta -i LSC.index -q "${id}" >> LSC.reverse.fasta
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done
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loginfo " --> $(fastaCount LSC.reverse.fasta) sequences"
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loginfo "Done"
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loginfo "merging both connected components for LCS..."
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fastarevcomp LSC.reverse.fasta >> LSC.direct.fasta
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loginfo " --> $(fastaCount LSC.direct.fasta) sequences in total"
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loginfo "Done"
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loginfo "Checking LCS homogeneity..."
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${PROG_DIR}/coorienteSC.sh LSC.direct.fasta 20000 ${ORG_LOGFILE} > LSC_RefDB.tgf
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${PROG_DIR}/cc.py LSC_RefDB.tgf > LSC_RefDB.cc
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NCC=$(awk '{print $1}' LSC_RefDB.cc | uniq | wc -l)
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if (( $NCC == 1 )); then
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loginfo " --> $NCC connected componants"
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else
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logwarning " --> $NCC connected componants"
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fi
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loginfo "Done"
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loginfo "Installing LCS reference databases..."
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cp LSC.direct.fasta "${IR_DATA_DIR}/LSC_RefDB.fasta"
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cp LSC_RefDB.tgf "${IR_DATA_DIR}/LSC_RefDB.tgf"
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loginfo "Done"
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#
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# Deals with Short Single Copies (SSC)
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#
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loginfo "Extracting Short Single Copies (SSC)..."
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${PROG_DIR}/extract_refSSC.sh ${VIRIDIPLANTAE} > SSC.fasta
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loginfo " --> $(fastaCount SSC.fasta) retreived sequences"
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loginfo "Done"
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loginfo "Building SSC coorientation graph..."
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${PROG_DIR}/coorienteSC.sh SSC.fasta 5000 ${ORG_LOGFILE} > SSC.tgf
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${PROG_DIR}/cc.py SSC.tgf > SSC.cc
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loginfo " --> $(awk '{print $1}' SSC.cc | uniq | wc -l) connected componants"
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loginfo "Done"
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loginfo "Indexing SSC..."
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fastaindex -f SSC.fasta -i SSC.index
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loginfo "Done"
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loginfo "Extracting main connected components for SSC..."
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rm -f SSC.direct.fasta
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touch SSC.direct.fasta
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for id in `awk '($1==0) {print $2}' SSC.cc`; do
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fastafetch -f SSC.fasta -i SSC.index -q "${id}" >> SSC.direct.fasta
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done
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loginfo " --> $(fastaCount SSC.direct.fasta) sequences"
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loginfo "Done"
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loginfo "Extracting second connected components for SSC..."
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rm -f SSC.reverse.fasta
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touch SSC.reverse.fasta
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for id in `awk '($1==1) {print $2}' SSC.cc`; do
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fastafetch -f SSC.fasta -i SSC.index -q "${id}" >> SSC.reverse.fasta
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done
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loginfo " --> $(fastaCount SSC.reverse.fasta) sequences"
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loginfo "Done"
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loginfo "merging both connected components for SSC..."
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fastarevcomp SSC.reverse.fasta >> SSC.direct.fasta
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loginfo " --> $(fastaCount SSC.direct.fasta) sequences in total"
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loginfo "Done"
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loginfo "Checking SSC homogeneity..."
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${PROG_DIR}/coorienteSC.sh SSC.direct.fasta 5000 ${ORG_LOGFILE} > SSC_RefDB.tgf
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${PROG_DIR}/cc.py SSC_RefDB.tgf > SSC_RefDB.cc
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NCC=$(awk '{print $1}' SSC_RefDB.cc | uniq | wc -l)
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if (( $NCC == 1 )); then
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loginfo " --> $NCC connected componants"
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else
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logwarning " --> $NCC connected componants"
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fi
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loginfo "Done"
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loginfo "Installing SSC reference databases..."
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cp SSC.direct.fasta "${IR_DATA_DIR}/SSC_RefDB.fasta"
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cp SSC_RefDB.tgf "${IR_DATA_DIR}/SSC_RefDB.tgf"
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loginfo "Done"
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loginfo "Installing blast version of the SC_RefDB reference databases..."
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cat "${IR_DATA_DIR}/LSC_RefDB.fasta" \
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"${IR_DATA_DIR}/SSC_RefDB.fasta" > SC_RefDB.fasta
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makeblastdb -in SC_RefDB.fasta \
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-dbtype nucl \
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-out "${IR_DATA_DIR}/SC_RefDB" >& /dev/null
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loginfo "Done"
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popTmpDir
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