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First version of if inverted repeat annotation tools

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Former-commit-id: 9d13deae459b086f11ba4f0f82aac899b4ff0fd9
Former-commit-id: 74a7f07d3fb26f6ce12808b8fe2dc7f176181285
This commit is contained in:
Eric Coissac
2015-10-08 17:38:01 -03:00
parent f901b87ccd
commit c402923d0f
5 changed files with 130 additions and 80 deletions
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detectors/ir/.DS_Store vendored Normal file
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detectors/ir/bin/go_ir.sh Executable file
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#!/bin/bash
#
# Annotate the Inverted Repeats of a plastide genome
#
#========================================================================================
#
# 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
SCRIPT_DIR="$(dirname ${BASH_SOURCE[0]})"
source ${SCRIPT_DIR}/../../normalize/lib/lookforIR.lib.sh
pushTmpDir ORG.ir
loginfo "Computing the genome size..."
genome_length=$(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 + $lenIR - 1"
beginLSC=1
let "endLSC=$posIR1-1"
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\""
popTmpDir
exit 0