CY_stuff/circos_script.shell at master · rtmag/CY_stuff · GitHub

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###################################################################################################################
# New Directory
rm -fr circos_Simulations/
mkdir circos_Simulations/
###################################################################################################################
# Delly
mkdir circos_Simulations/delly_sim1
mkdir circos_Simulations/delly_sim1/data
cp circos_backbone/data/karyotype.txt circos_Simulations/delly_sim1/data/
cp circos_backbone/*conf circos_Simulations/delly_sim1/
#
more Simulations/delly_sim1/dell_sim1_breakends.bed|cut -f1-6|perl -pe 's/chr/hs/g' \
> circos_Simulations/delly_sim1/data/insertions.bed
more Simulations/delly_sim1/dell_sim1_deletions.bed|cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/delly_sim1/data/deletions.bed
more Simulations/delly_sim1/dell_sim1_duplication_breakpoints.bed|cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/delly_sim1/data/tandemDuplications.bed
more Simulations/delly_sim1/dell_sim1_insertion_breakpoints.bed|cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/delly_sim1/data/viralinsertions.bed
more Simulations/delly_sim1/dell_sim1_inversions.bed|cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/delly_sim1/data/inversions.bed
#
circos -conf circos_Simulations/delly_sim1/circos.conf -outputfile circos_Simulations/delly_sim1/delly_sim1
###################################################################################################################
# Ground TRUTH
mkdir circos_Simulations/groundtruth_sim1
mkdir circos_Simulations/groundtruth_sim1/data
cp circos_backbone/data/karyotype.txt circos_Simulations/groundtruth_sim1/data/
cp circos_backbone/*conf circos_Simulations/groundtruth_sim1/
#
more Simulations/groundtruth_sim1/sim1_insertions.bed|cut -f1-6|perl -pe 's/chr/hs/g' \
> circos_Simulations/groundtruth_sim1/data/insertions.bed

more Simulations/groundtruth_sim1/sim1_deletions.bed|cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/groundtruth_sim1/data/deletions.bed

more Simulations/groundtruth_sim1/sim1_tandemDuplications.bed|cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/groundtruth_sim1/data/tandemDuplications.bed

more Simulations/groundtruth_sim1/sim1_viralinsertions.bed|cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/groundtruth_sim1/data/viralinsertions.bed

more Simulations/groundtruth_sim1/sim1_inversions.bed|cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/groundtruth_sim1/data/inversions.bed
#
circos -conf circos_Simulations/groundtruth_sim1/circos.conf -outputfile circos_Simulations/groundtruth_sim1/groundtruth_sim1
###################################################################################################################
# Ground TRUTH
mkdir circos_Simulations/hybridseek_sim1
mkdir circos_Simulations/hybridseek_sim1/data
cp circos_backbone/data/karyotype.txt circos_Simulations/hybridseek_sim1/data/
cp circos_backbone/*conf circos_Simulations/hybridseek_sim1/
#
more Simulations/hybridseek_sim1/hs_sim1_insertions_breakpoints.bed |cut -f1-6|perl -pe 's/chr/hs/g' \
> circos_Simulations/hybridseek_sim1/data/insertions.bed

more Simulations/hybridseek_sim1/hs_sim1_translocation_breakpoints.bed |cut -f1-6|perl -pe 's/chr/hs/g' \
>> circos_Simulations/hybridseek_sim1/data/insertions.bed

more Simulations/hybridseek_sim1/hs_sim1_deletions.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/hybridseek_sim1/data/deletions.bed

more Simulations/hybridseek_sim1/hs_sim1_tandemDuplication_breakpoints.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/hybridseek_sim1/data/tandemDuplications.bed

more Simulations/hybridseek_sim1/hs_sim1_novelinsertions_breakpoints.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/hybridseek_sim1/data/viralinsertions.bed

more Simulations/hybridseek_sim1/hs_sim1_inversions.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/hybridseek_sim1/data/inversions.bed
#
circos -conf circos_Simulations/hybridseek_sim1/circos.conf -outputfile circos_Simulations/hybridseek_sim1/hybridseek_sim1
#
###################################################################################################################
# NanoSV
mkdir circos_Simulations/nanoSV_sim1
mkdir circos_Simulations/nanoSV_sim1/data
cp circos_backbone/data/karyotype.txt circos_Simulations/nanoSV_sim1/data/
cp circos_backbone/*conf circos_Simulations/nanoSV_sim1/
#
more Simulations/nanoSV_sim1/nanosv_sim1_breakends.bed |cut -f1-6|perl -pe 's/chr/hs/g' \
> circos_Simulations/nanoSV_sim1/data/insertions.bed

more Simulations/nanoSV_sim1/nanosv_sim1_deletions.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/nanoSV_sim1/data/deletions.bed

more Simulations/nanoSV_sim1/nanosv_sim1_duplication_breakpoints.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/nanoSV_sim1/data/tandemDuplications.bed

more Simulations/nanoSV_sim1/nanosv_sim1_insertion_breakpoints.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/nanoSV_sim1/data/viralinsertions.bed

more  |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/nanoSV_sim1/data/inversions.bed
#
circos -conf circos_Simulations/nanoSV_sim1/circos.conf -outputfile circos_Simulations/nanoSV_sim1/nanoSV_sim1
#
###################################################################################################################
# Novobreak
mkdir circos_Simulations/novobreak_sim1
mkdir circos_Simulations/novobreak_sim1/data
cp circos_backbone/data/karyotype.txt circos_Simulations/novobreak_sim1/data/
cp circos_backbone/*conf circos_Simulations/novobreak_sim1/
#
more Simulations/novobreak_sim1/novo_sim1_translocation_breakpoints.bed |cut -f1-6|perl -pe 's/chr/hs/g' \
> circos_Simulations/novobreak_sim1/data/insertions.bed

more Simulations/novobreak_sim1/novo_sim1_deletions.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/novobreak_sim1/data/deletions.bed

more Simulations/novobreak_sim1/novo_sim1_tandemDuplication_breakpoints.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/novobreak_sim1/data/tandemDuplications.bed

more  |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/novobreak_sim1/data/viralinsertions.bed

more Simulations/novobreak_sim1/novo_sim1_inversions.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/novobreak_sim1/data/inversions.bed
#
circos -conf circos_Simulations/novobreak_sim1/circos.conf -outputfile circos_Simulations/novobreak_sim1/novobreak_sim1
#
###################################################################################################################
# Picky
mkdir circos_Simulations/picky_sim1
mkdir circos_Simulations/picky_sim1/data
cp circos_backbone/data/karyotype.txt circos_Simulations/picky_sim1/data/
cp circos_backbone/*conf circos_Simulations/picky_sim1/
#
more Simulations/picky_sim1/pick_sim1_breakends.bed |cut -f1-6|perl -pe 's/chr/hs/g' \
> circos_Simulations/picky_sim1/data/insertions.bed

more Simulations/picky_sim1/pick_sim1_deletions.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/picky_sim1/data/deletions.bed

more Simulations/picky_sim1/pick_sim1_duplication_breakpoints.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/picky_sim1/data/tandemDuplications.bed

more Simulations/picky_sim1/pick_sim1_insertion_breakpoints.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/picky_sim1/data/viralinsertions.bed

more Simulations/picky_sim1/pick_sim1_inversions.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/picky_sim1/data/inversions.bed
#
circos -conf circos_Simulations/picky_sim1/circos.conf -outputfile circos_Simulations/picky_sim1/picky_sim1
#
####################################################################################################################
# Sniffles
mkdir circos_Simulations/sniffles_sim1
mkdir circos_Simulations/sniffles_sim1/data
cp circos_backbone/data/karyotype.txt circos_Simulations/sniffles_sim1/data/
cp circos_backbone/*conf circos_Simulations/sniffles_sim1/
#
more Simulations/sniffles_sim1/sniff_sim1_translocation_breakpoints.bed |cut -f1-6|perl -pe 's/chr/hs/g' \
> circos_Simulations/sniffles_sim1/data/insertions.bed

more Simulations/sniffles_sim1/sniff_sim1_deletions.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/sniffles_sim1/data/deletions.bed

more Simulations/sniffles_sim1/sniff_sim1_del_or_inv.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' >> circos_Simulations/sniffles_sim1/data/deletions.bed

more Simulations/sniffles_sim1/sniff_sim1_duplication_breakpoints.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/sniffles_sim1/data/tandemDuplications.bed

more Simulations/sniffles_sim1/sniff_sim1_dup_or_ins.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' >> circos_Simulations/sniffles_sim1/data/tandemDuplications.bed

more Simulations/sniffles_sim1/sniff_sim1_insertion_breakpoints.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/sniffles_sim1/data/viralinsertions.bed

more Simulations/sniffles_sim1/sniff_sim1_inversions.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' > circos_Simulations/sniffles_sim1/data/inversions.bed

more Simulations/sniffles_sim1/sniff_sim1_inv_or_dup.bed |cut -f1-3| \
perl -pe 's/chr/hs/g'|perl -pe 's/\n/\t10\n/g' >> circos_Simulations/sniffles_sim1/data/inversions.bed
#
circos -conf circos_Simulations/sniffles_sim1/circos.conf -outputfile circos_Simulations/sniffles_sim1/sniffles_sim1
#
####################################################################################################################
mkdir circos_Simulations/circos_plot
cp circos_Simulations/*/*svg circos_Simulations/circos_plot
cp circos_Simulations/*/*png circos_Simulations/circos_plot
###############