Eric Coissac
c402923d0f
Former-commit-id: 9d13deae459b086f11ba4f0f82aac899b4ff0fd9 Former-commit-id: 74a7f07d3fb26f6ce12808b8fe2dc7f176181285
65 lines
1.8 KiB
Bash
Executable File
65 lines
1.8 KiB
Bash
Executable File
#!/bin/bash
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#
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# Annotate the Inverted Repeats of a plastide genome
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#
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#========================================================================================
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#
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# The SSC and LSC are approximatively mapped by similarity with a reference database
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# Inverted repeats (IRs) are identified for maximizing the segregation between
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# LSC and SSC match
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#
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#
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# go_normalize.sh <FASTAFILE>
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#
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# - <FASTAFILE> : The fasta file containing the genome to normalize
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#
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# Results are printed to the standart output
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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 ${SCRIPT_DIR}/../../normalize/lib/lookforIR.lib.sh
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pushTmpDir ORG.ir
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loginfo "Computing the genome size..."
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genome_length=$(seqlength $QUERY)
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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]} + ${IR[7]} ) / 2 "
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let "endIR2=$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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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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popTmpDir
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exit 0
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