Add a patch for chloroplast annotation when no inverted repeats are
detected Former-commit-id: 7e3ddd41cf0d0788223382fedbf45b183974233e Former-commit-id: e5a8ceb825f78d243e37d22cd6b2e91f403c0ee8
This commit is contained in:
@ -29,35 +29,37 @@ pushTmpDir ORG.ir
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loginfo " --> $genome_length bp"
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loginfo "Done"
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IR=( $(lookForIR ${QUERY}) )
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posIR1=${IR[4]}
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posIR2=${IR[6]}
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let "lenIR= ( ${IR[5]} + ${IR[7]} ) / 2 "
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IRDetected=1
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IR=( $(lookForIR ${QUERY}) ) || IRDetected=0
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let "endIR2=$posIR2 + $lenIR - 1"
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let "endIR1=$posIR1 + $lenIR - 1"
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beginLSC=1
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let "endLSC=$posIR1-1"
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let "beginSSC=$endIR1+1"
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let "endSSC=$posIR2-1"
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if (( IRDetected == 1 )) ; then
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posIR1=${IR[4]}
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posIR2=${IR[6]}
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let "lenIR= ( ${IR[5]} + ${IR[7]} ) / 2 "
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let "endIR2=$posIR2 + $lenIR - 1"
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let "endIR1=$posIR1 + $lenIR - 1"
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beginLSC=1
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let "endLSC=$posIR1-1"
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echo "FT misc_feature ${beginLSC}..${endLSC}"
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echo "FT /note=\"large single copy region (LSC)\""
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echo "FT repeat_region ${posIR1}..${endIR1}"
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echo "FT /rpt_type=INVERTED"
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echo "FT /note=\"left inverted repeat B; IRB\""
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echo "FT misc_feature ${beginSSC}..${endSSC}"
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echo "FT /note=\"small single copy region (SSC)\""
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echo "FT repeat_region ${posIR2}..${endIR2}"
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echo "FT /rpt_type=INVERTED"
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echo "FT /note=\"left inverted repeat A; IRA\""
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let "beginSSC=$endIR1+1"
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let "endSSC=$posIR2-1"
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echo "FT misc_feature ${beginLSC}..${endLSC}"
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echo "FT /note=\"large single copy region (LSC)\""
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echo "FT repeat_region ${posIR1}..${endIR1}"
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echo "FT /rpt_type=INVERTED"
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echo "FT /note=\"left inverted repeat B; IRB\""
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echo "FT misc_feature ${beginSSC}..${endSSC}"
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echo "FT /note=\"small single copy region (SSC)\""
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echo "FT repeat_region ${posIR2}..${endIR2}"
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echo "FT /rpt_type=INVERTED"
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echo "FT /note=\"left inverted repeat A; IRA\""
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fi
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popTmpDir
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@ -41,128 +41,134 @@ pushTmpDir ORG.normalize
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loginfo " --> $genome_length bp"
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loginfo "Done"
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IR=( $(lookForIR ${QUERY}) )
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IRDetected=1
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IR=( $(lookForIR ${QUERY}) ) || IRDetected=0
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posIR1=${IR[4]}
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posIR2=${IR[6]}
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if (( IRDetected == 1 )) ; then
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let "lenIR= ( ${IR[5]} + ${IR[7]} ) / 2 "
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let "endIR2=$posIR2 + $lenIR - 1"
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let "endIR1=$posIR1 + $lenIR - 1"
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if (( "$endIR2" >= "$genome_length" )) ; then
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loginfo "IRB is at the end of the original sequence"
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posIR1=${IR[4]}
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posIR2=${IR[6]}
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#
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# We just move the IRB at the begining of the sequence
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#
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# Extract the IRB sequence
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let "posCut=($endIR1+$posIR2)/2"
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cutseq ${QUERY} ${posCut} ${genome_length} > ${tmpfasta1}
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# Append the remaining part of the genome
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let "posCut=$posCut-1"
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cutseq ${QUERY} 1 ${posCut} >> ${tmpfasta1}
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# merges both the parts
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joinfasta ${tmpfasta1} > ${tmpfasta2}
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rm -f ${tmpfasta1}
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QUERY=${tmpfasta2}
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loginfo "Recomputing location of the IR..."
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declare -a IR=( $(lookForIR ${QUERY}) )
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loginfo "Done"
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posIR1="${IR[4]}"
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posIR2="${IR[6]}"
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let "lenIR=(${IR[5]} + ${IR[7]}) / 2 "
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let "lenIR= ( ${IR[5]} + ${IR[7]} ) / 2 "
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let "endIR2=$posIR2 + $lenIR - 1"
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let "endIR1=$posIR1 + $lenIR - 1"
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fi
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if (( "$endIR2" >= "$genome_length" )) ; then
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loginfo "IRB is at the end of the original sequence"
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#
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# We just move the IRB at the begining of the sequence
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#
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# Extract the IRB sequence
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let "posCut=($endIR1+$posIR2)/2"
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cutseq ${QUERY} ${posCut} ${genome_length} > ${tmpfasta1}
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tmpIR1="tmp_$$_IR1.fasta"
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tmpIR2="tmp_$$_IR2.fasta"
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# Append the remaining part of the genome
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let "posCut=$posCut-1"
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cutseq ${QUERY} 1 ${posCut} >> ${tmpfasta1}
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# merges both the parts
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joinfasta ${tmpfasta1} > ${tmpfasta2}
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rm -f ${tmpfasta1}
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QUERY=${tmpfasta2}
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#enregistre les deux fragments IRa et IRb complet
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cutseq ${QUERY} ${posIR1} ${endIR1} > ${tmpIR1}
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cutseq ${QUERY} ${posIR2} ${endIR2} > ${tmpIR2}
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let "lenSC1=$posIR1 -1 + ($genome_length - endIR2)"
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let "lenSC2=$posIR2 - $endIR1"
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center="${IR[0]}"
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loginfo "Recomputing location of the IR..."
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declare -a IR=( $(lookForIR ${QUERY}) )
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loginfo "Done"
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posIR1="${IR[4]}"
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posIR2="${IR[6]}"
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let "lenIR=(${IR[5]} + ${IR[7]}) / 2 "
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tmpLSC="tmp_$$_LSC.fasta"
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tmpSSC="tmp_$$_SSC.fasta"
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# Extract the central SC present in between the two IRs
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# considering it as LSC
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let "beginLSC=$endIR1+1"
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let "endLSC=$posIR2-1"
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cutseq ${QUERY} ${beginLSC} ${endLSC} > ${tmpLSC}
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strandLSC="${IR[1]}"
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# Extract the external SC present in two parts
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# Considering it as SSC
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let "beginSSC=$endIR2+1"
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cutseq ${QUERY} ${beginSSC} ${genome_length} > ${tmpSSC}
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let "endSSC=$posIR1-1"
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cutseq ${QUERY} 1 ${endSSC} >> ${tmpSSC}
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joinfasta ${tmpSSC} > ${tmpfasta1}
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mv ${tmpfasta1} ${tmpSSC}
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strandSSC="${IR[3]}"
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if [[ "$center" == "SSC" ]]; then
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# Actually this is the oposite LSC is SSC and SSC is LSC
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# Exchanges the SSC and LSC sequences
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mv ${tmpSSC} ${tmpfasta1}
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mv ${tmpLSC} ${tmpSSC}
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mv ${tmpfasta1} ${tmpLSC}
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let "endIR2=$posIR2 + $lenIR - 1"
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let "endIR1=$posIR1 + $lenIR - 1"
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fi
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# Exchanges the IRa and IRb sequences
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mv ${tmpIR1} ${tmpfasta1}
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mv ${tmpIR2} ${tmpIR1}
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mv ${tmpfasta1} ${tmpIR2}
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tmpIR1="tmp_$$_IR1.fasta"
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tmpIR2="tmp_$$_IR2.fasta"
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# Exchanges the strand of both the Single copies
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tmp=${strandSSC}
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strandSSC=${strandLSC}
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strandLSC=${tmp}
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#enregistre les deux fragments IRa et IRb complet
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cutseq ${QUERY} ${posIR1} ${endIR1} > ${tmpIR1}
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cutseq ${QUERY} ${posIR2} ${endIR2} > ${tmpIR2}
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fi
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let "lenSC1=$posIR1 -1 + ($genome_length - endIR2)"
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let "lenSC2=$posIR2 - $endIR1"
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center="${IR[0]}"
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tmpLSC="tmp_$$_LSC.fasta"
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tmpSSC="tmp_$$_SSC.fasta"
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# Extract the central SC present in between the two IRs
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# considering it as LSC
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# Reverse complement the SSC if needed
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if [[ "${strandSSC}" == "-" ]]; then
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fastarevcomp -f ${tmpSSC} > ${tmpfasta1}
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let "beginLSC=$endIR1+1"
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let "endLSC=$posIR2-1"
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cutseq ${QUERY} ${beginLSC} ${endLSC} > ${tmpLSC}
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strandLSC="${IR[1]}"
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# Extract the external SC present in two parts
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# Considering it as SSC
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let "beginSSC=$endIR2+1"
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cutseq ${QUERY} ${beginSSC} ${genome_length} > ${tmpSSC}
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let "endSSC=$posIR1-1"
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cutseq ${QUERY} 1 ${endSSC} >> ${tmpSSC}
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joinfasta ${tmpSSC} > ${tmpfasta1}
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mv ${tmpfasta1} ${tmpSSC}
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fi
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strandSSC="${IR[3]}"
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# Reverse complement the LSC if needed
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if [[ "${strandLSC}" == "-" ]]; then
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fastarevcomp -f ${tmpLSC} > ${tmpfasta1}
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mv ${tmpfasta1} ${tmpLSC}
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fi
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if [[ "$center" == "SSC" ]]; then
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# Actually this is the oposite LSC is SSC and SSC is LSC
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# Merges the four parts of the genome.
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cat ${tmpLSC} ${tmpIR2} ${tmpSSC} ${tmpIR1} | joinfasta
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# Exchanges the SSC and LSC sequences
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mv ${tmpSSC} ${tmpfasta1}
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mv ${tmpLSC} ${tmpSSC}
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mv ${tmpfasta1} ${tmpLSC}
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# Exchanges the IRa and IRb sequences
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mv ${tmpIR1} ${tmpfasta1}
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mv ${tmpIR2} ${tmpIR1}
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mv ${tmpfasta1} ${tmpIR2}
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# Exchanges the strand of both the Single copies
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tmp=${strandSSC}
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strandSSC=${strandLSC}
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strandLSC=${tmp}
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fi
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# Reverse complement the SSC if needed
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if [[ "${strandSSC}" == "-" ]]; then
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fastarevcomp -f ${tmpSSC} > ${tmpfasta1}
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mv ${tmpfasta1} ${tmpSSC}
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fi
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# Reverse complement the LSC if needed
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if [[ "${strandLSC}" == "-" ]]; then
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fastarevcomp -f ${tmpLSC} > ${tmpfasta1}
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mv ${tmpfasta1} ${tmpLSC}
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fi
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# Merges the four parts of the genome.
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cat ${tmpLSC} ${tmpIR2} ${tmpSSC} ${tmpIR1} | joinfasta
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else
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# No IR detected --> normalization has no effect
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cat ${QUERY}
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fi
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popTmpDir
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exit 0
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@ -38,9 +38,16 @@ function lookForIR {
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loginfo "Looking for long inverted repeats..."
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repseek -c -p 0.001 -i ${QUERY} 2>> /dev/null > ${REPEATS}
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loginfo " --> $(wc -l ${REPEATS} | awk '{print $1}') repeats identified"
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nrepeat="$(wc -l ${REPEATS} | awk '{print $1}')"
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loginfo "Done"
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if (( nrepeat == 0 )) ; then
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logwarning "No inverted repeat identified"
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return 1
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fi
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loginfo " --> ${nrepeat} repeats identified"
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loginfo "Marking and selecting the best inverted repeat..."
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local IR=( $(${SELECTIR} ${MATCHES} ${REPEATS}) )
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loginfo "Done"
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Block a user