efb9949075
Former-commit-id: a72f30f90d22cc3c7ff6059e0254e47911bb5af1 Former-commit-id: db0264bdbe5136b6e6dc44e4788175a257439643
170 lines
3.9 KiB
Bash
Executable File
170 lines
3.9 KiB
Bash
Executable File
#!/bin/bash
|
|
#
|
|
# NORMALISATION D'UN PLASTIDE
|
|
#
|
|
#========================================================================================
|
|
#
|
|
# Normalize the way the chloroplaste genome sequence is linearized in the fasta file
|
|
# The normalized sequence is:
|
|
#
|
|
# LSC + IRB + SSC + IRA
|
|
#
|
|
# The SSC and LSC are approximatively mapped by similarity with a reference database
|
|
# Inverted repeats (IRs) are identified for maximizing the segregation between
|
|
# LSC and SSC match
|
|
#
|
|
#
|
|
# go_normalize.sh <FASTAFILE>
|
|
#
|
|
# - <FASTAFILE> : The fasta file containing the genome to normalize
|
|
#
|
|
# Results are printed to the standart output
|
|
#
|
|
#========================================================================================
|
|
|
|
# -- CAUTION -- Works as long than the script
|
|
# is not called through a symlink
|
|
THIS_DIR="$(dirname ${BASH_SOURCE[0]})"
|
|
source ${THIS_DIR}/../lib/lookforIR.lib.sh
|
|
|
|
ORG_DEBUG=1
|
|
|
|
pushTmpDir ORG.normalize
|
|
|
|
tmpfasta1="tmp_$$_1.fasta"
|
|
tmpfasta2="tmp_$$_2.fasta"
|
|
|
|
logdebug "Running on : $QUERY"
|
|
|
|
loginfo "Computing the genome size..."
|
|
genome_length=$(seqlength $QUERY)
|
|
loginfo " --> $genome_length bp"
|
|
loginfo "Done"
|
|
|
|
IR=( $(lookForIR ${QUERY}) )
|
|
|
|
posIR1=${IR[4]}
|
|
posIR2=${IR[6]}
|
|
|
|
let "lenIR= ( ${IR[5]} + ${IR[7]} ) / 2 "
|
|
|
|
let "endIR2=$posIR2 + $lenIR - 1"
|
|
let "endIR1=$posIR1 + $lenIR - 1"
|
|
|
|
if (( "$endIR2" >= "$genome_length" )) ; then
|
|
loginfo "IRB is at the end of the original sequence"
|
|
|
|
#
|
|
# We just move the IRB at the begining of the sequence
|
|
#
|
|
|
|
# Extract the IRB sequence
|
|
let "posCut=($endIR1+$posIR2)/2"
|
|
cutseq ${QUERY} ${posCut} ${genome_length} > ${tmpfasta1}
|
|
|
|
# Append the remaining part of the genome
|
|
let "posCut=$posCut-1"
|
|
cutseq ${QUERY} 1 ${posCut} >> ${tmpfasta1}
|
|
|
|
# merges both the parts
|
|
joinfasta ${tmpfasta1} > ${tmpfasta2}
|
|
rm -f ${tmpfasta1}
|
|
QUERY=${tmpfasta2}
|
|
|
|
loginfo "Recomputing location of the IR..."
|
|
declare -a IR=( $(lookForIR ${QUERY}) )
|
|
loginfo "Done"
|
|
|
|
posIR1="${IR[4]}"
|
|
posIR2="${IR[6]}"
|
|
|
|
let "lenIR=(${IR[5]} + ${IR[7]}) / 2 "
|
|
|
|
let "endIR2=$posIR2 + $lenIR - 1"
|
|
let "endIR1=$posIR1 + $lenIR - 1"
|
|
|
|
fi
|
|
|
|
tmpIR1="tmp_$$_IR1.fasta"
|
|
tmpIR2="tmp_$$_IR2.fasta"
|
|
|
|
#enregistre les deux fragments IRa et IRb complet
|
|
cutseq ${QUERY} ${posIR1} ${endIR1} > ${tmpIR1}
|
|
cutseq ${QUERY} ${posIR2} ${endIR2} > ${tmpIR2}
|
|
|
|
let "lenSC1=$posIR1 -1 + ($genome_length - endIR2)"
|
|
let "lenSC2=$posIR2 - $endIR1"
|
|
|
|
center="${IR[0]}"
|
|
|
|
tmpLSC="tmp_$$_LSC.fasta"
|
|
tmpSSC="tmp_$$_SSC.fasta"
|
|
|
|
# Extract the first SC present in between the two IRs
|
|
# considering it as LSC
|
|
|
|
let "beginLSC=$endIR1+1"
|
|
let "endLSC=$posIR2-1"
|
|
cutseq ${QUERY} ${beginLSC} ${endLSC} > ${tmpLSC}
|
|
|
|
strandLSC="${IR[1]}"
|
|
|
|
|
|
# Extract the second SC present in two parts
|
|
# Considering it as SSC
|
|
|
|
let "beginSSC=$endIR2+1"
|
|
cutseq ${QUERY} ${beginSSC} ${genome_length} > ${tmpSSC}
|
|
|
|
let "endSSC=$posIR1-1"
|
|
cutseq ${QUERY} 1 ${endSSC} >> ${tmpSSC}
|
|
|
|
joinfasta ${tmpSSC} > ${tmpfasta1}
|
|
mv ${tmpfasta1} ${tmpSSC}
|
|
|
|
strandSSC="${IR[3]}"
|
|
|
|
|
|
|
|
if [[ "$center" == "SSC" ]]; then
|
|
|
|
# Actually this is the oposite LSC is SSC and SSC is LSC
|
|
|
|
# Exchange the SSC and LSC sequences
|
|
mv ${tmpSSC} ${tmpfasta1}
|
|
mv ${tmpLSC} ${tmpSSC}
|
|
mv ${tmpfasta1} ${tmpLSC}
|
|
|
|
# Exchange the IRa and IRb sequences
|
|
mv ${tmpIR1} ${tmpfasta1}
|
|
mv ${tmpIR2} ${tmpIR1}
|
|
mv ${tmpfasta1} ${tmpIR2}
|
|
|
|
tmp=${strandSSC}
|
|
strandSSC=${strandLSC}
|
|
strandLSC=${tmp}
|
|
|
|
fi
|
|
|
|
# Reverse complement the SSC if needed
|
|
if [[ "${strandSSC}" == "-" ]]; then
|
|
fastarevcomp -f ${tmpSSC} > ${tmpfasta1}
|
|
mv ${tmpfasta1} ${tmpSSC}
|
|
fi
|
|
|
|
# Reverse complement the LSC if needed
|
|
if [[ "${strandLSC}" == "-" ]]; then
|
|
fastarevcomp -f ${tmpLSC} > ${tmpfasta1}
|
|
mv ${tmpfasta1} ${tmpLSC}
|
|
fi
|
|
|
|
# Merges the four parts of the genome.
|
|
cat ${tmpLSC} ${tmpIR2} ${tmpSSC} ${tmpIR1} | joinfasta
|
|
|
|
|
|
|
|
popTmpDir
|
|
|
|
exit 0
|
|
|