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Patch bug in the inverted repeats annotation

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Realize the annotation on the normalized chromosome


Former-commit-id: 73e4e016d7bfe23fc92e4071efb0a4629eb8e21f
Former-commit-id: d44249c0d078d475ca80386bb428fb660289b0dd
This commit is contained in:
Eric Coissac
2015-11-09 17:03:22 +01:00
parent 58e99a81eb
commit 195739b5f8
4 changed files with 53 additions and 20 deletions
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11
detectors/normalize/bin/go_normalize.sh
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@@ -100,7 +100,7 @@ pushTmpDir ORG.normalize
tmpLSC="tmp_$$_LSC.fasta"
tmpSSC="tmp_$$_SSC.fasta"
# Extract the first SC present in between the two IRs
# Extract the central SC present in between the two IRs
# considering it as LSC
let "beginLSC=$endIR1+1"
@@ -110,7 +110,7 @@ pushTmpDir ORG.normalize
strandLSC="${IR[1]}"
# Extract the second SC present in two parts
# Extract the external SC present in two parts
# Considering it as SSC
let "beginSSC=$endIR2+1"
@@ -130,16 +130,17 @@ pushTmpDir ORG.normalize
# Actually this is the oposite LSC is SSC and SSC is LSC
# Exchange the SSC and LSC sequences
# Exchanges the SSC and LSC sequences
mv ${tmpSSC} ${tmpfasta1}
mv ${tmpLSC} ${tmpSSC}
mv ${tmpfasta1} ${tmpLSC}
# Exchange the IRa and IRb sequences
# Exchanges the IRa and IRb sequences
mv ${tmpIR1} ${tmpfasta1}
mv ${tmpIR2} ${tmpIR1}
mv ${tmpfasta1} ${tmpIR2}
# Exchanges the strand of both the Single copies
tmp=${strandSSC}
strandSSC=${strandLSC}
strandLSC=${tmp}
@@ -161,7 +162,7 @@ pushTmpDir ORG.normalize
# Merges the four parts of the genome.
cat ${tmpLSC} ${tmpIR2} ${tmpSSC} ${tmpIR1} | joinfasta
exit 1
popTmpDir