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Add a patch for chloroplast annotation when no inverted repeats are

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Former-commit-id: 7e3ddd41cf0d0788223382fedbf45b183974233e
Former-commit-id: e5a8ceb825f78d243e37d22cd6b2e91f403c0ee8
This commit is contained in:
Eric Coissac
2016-05-02 15:32:28 +02:00
parent 8a1a1d57ba
commit 466308267e
3 changed files with 146 additions and 131 deletions
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54
detectors/ir/bin/go_ir.sh
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@ -29,35 +29,37 @@ pushTmpDir ORG.ir
loginfo " --> $genome_length bp"
loginfo "Done"
IR=( $(lookForIR ${QUERY}) )
posIR1=${IR[4]}
posIR2=${IR[6]}
let "lenIR= ( ${IR[5]} + ${IR[7]} ) / 2 "
IRDetected=1
IR=( $(lookForIR ${QUERY}) ) || IRDetected=0
let "endIR2=$posIR2 + $lenIR - 1"
let "endIR1=$posIR1 + $lenIR - 1"
beginLSC=1
let "endLSC=$posIR1-1"
let "beginSSC=$endIR1+1"
let "endSSC=$posIR2-1"
if (( IRDetected == 1 )) ; then
posIR1=${IR[4]}
posIR2=${IR[6]}
let "lenIR= ( ${IR[5]} + ${IR[7]} ) / 2 "
let "endIR2=$posIR2 + $lenIR - 1"
let "endIR1=$posIR1 + $lenIR - 1"
beginLSC=1
let "endLSC=$posIR1-1"
echo "FT misc_feature ${beginLSC}..${endLSC}"
echo "FT /note=\"large single copy region (LSC)\""
echo "FT repeat_region ${posIR1}..${endIR1}"
echo "FT /rpt_type=INVERTED"
echo "FT /note=\"left inverted repeat B; IRB\""
echo "FT misc_feature ${beginSSC}..${endSSC}"
echo "FT /note=\"small single copy region (SSC)\""
echo "FT repeat_region ${posIR2}..${endIR2}"
echo "FT /rpt_type=INVERTED"
echo "FT /note=\"left inverted repeat A; IRA\""
let "beginSSC=$endIR1+1"
let "endSSC=$posIR2-1"
echo "FT misc_feature ${beginLSC}..${endLSC}"
echo "FT /note=\"large single copy region (LSC)\""
echo "FT repeat_region ${posIR1}..${endIR1}"
echo "FT /rpt_type=INVERTED"
echo "FT /note=\"left inverted repeat B; IRB\""
echo "FT misc_feature ${beginSSC}..${endSSC}"
echo "FT /note=\"small single copy region (SSC)\""
echo "FT repeat_region ${posIR2}..${endIR2}"
echo "FT /rpt_type=INVERTED"
echo "FT /note=\"left inverted repeat A; IRA\""
fi
popTmpDir