Skip to content

Update HBVIF.v0.2.1.sh #2

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
DomeJoyce wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Update HBVIF.v0.2.1.sh #2

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 13 additions & 13 deletions HBVIF.v0.1.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -445,13 +445,13 @@ echo -e $RED "### Running the last round of assembly pr integration site event
for i in *assembly_2.fasta*; do echo $i; cd-hit -i $i -o $i".cdhit.fasta"; done

for f in *.clstr ; do rm "$f"; done
ls *.cdhit.fasta | paste - - | while read line; do awk '{split(FILENAME,a,"."); print $0 > a[1]".final_assembly_3.fasta"}' $line ; done
for f in $(*.cdhit.fasta | paste - -); do awk '{split(FILENAME,a,"."); print $0 > a[1]".final_assembly_3.fasta"}' $f ; done

for i in *.final_assembly_3.fasta; do echo $i; awk '{if (/^>/) {f++} ; split(FILENAME,a,".") ; print > a[1]"."f".last.fasta"}' $i ; done
for f in *.final_assembly_3.fasta; do echo $f; awk '{if (/^>/) {f++} ; split(FILENAME,a,".") ; print > a[1]"."f".last.fasta"}' $f ; done

mkdir -p final_assembled_to_blast

mv *.last.fasta final_assembled_to_blast/
for f in *.last.fasta; do mv $f final_assembled_to_blast/ ; done

cd final_assembled_to_blast/

Expand All @@ -465,27 +465,27 @@ echo -e $RED "########## Performing BLAST iteration per integration site #######
echo -e LCYAN "This can take very long time, depending on the total number of integration sites found. Please be patient" $Z
numberOfSamples=$(ls *.fasta | wc -l)
COUNTER=0
ls *.fasta | while read line; do
for i in *.fasta ; do
let COUNTER+=1
echo $line", which is the integration event "$COUNTER" out of "$numberOfSamples
blastn -task blastn-short -dust no -soft_masking false -word_size 7 -num_threads $threads -max_target_seqs 2000 -db ../../genome/HG_HBV -query $line -outfmt 6 -penalty -3 -reward 2 -gapopen 5 -gapextend 2 | awk 'BEGIN {FS="\t";OFS = "\t"} {print $2,$9,$10,$7,$8}' > $line.intermediate.blast.out
echo $i", which is the integration event "$COUNTER" out of "$numberOfSamples
blastn -task blastn-short -dust no -soft_masking false -word_size 7 -num_threads $threads -max_target_seqs 2000 -db ../../genome/HG_HBV -query $i -outfmt 6 -penalty -3 -reward 2 -gapopen 5 -gapextend 2 | awk 'BEGIN {FS="\t";OFS = "\t"} {print $2,$9,$10,$7,$8}' > $i.intermediate.blast.out
done
echo -e $LRED "## Collecting and sorting BLAST results ###" $Z

ls *.intermediate.blast.out | while read line; do grep "$virus" $line | head -n 1 > $line.HBV; done
for f in *.intermediate.blast.out ; do grep "$virus" $f | head -n 1 > $f.HBV; done

ls *.intermediate.blast.out | while read line; do E=$(echo $line | cut -f1 -d "."); C=$(cat ../../SA_primary_secondary_no_HBV.bed | awk -F '\t' -v E=$E '{split($4,a,";");if(a[1]==E) print $1}'); S=$(cat ../../SA_primary_secondary_no_HBV.bed | awk -F '\t' -v E=$E '{split($4,a,";");if(a[1]==E) print $2}');F=$(cat ../../SA_primary_secondary_no_HBV.bed | awk -F '\t' -v E=$E '{split($4,a,";");if(a[1]==E) print $3}'); awk -F '\t' -v C="$C" -v S="$S" -v F="$F" '{if($1==C && $2>=S-100 && $3<=F+100) print $0}' $line | head -n1 > $line.HUMAN; done
for line in *.intermediate.blast.out ; do E=$(echo $line | cut -f1 -d "."); C=$(cat ../../SA_primary_secondary_no_HBV.bed | awk -F '\t' -v E=$E '{split($4,a,";");if(a[1]==E) print $1}'); S=$(cat ../../SA_primary_secondary_no_HBV.bed | awk -F '\t' -v E=$E '{split($4,a,";");if(a[1]==E) print $2}');F=$(cat ../../SA_primary_secondary_no_HBV.bed | awk -F '\t' -v E=$E '{split($4,a,";");if(a[1]==E) print $3}'); awk -F '\t' -v C="$C" -v S="$S" -v F="$F" '{if($1==C && $2>=S-100 && $3<=F+100) print $0}' $line | head -n1 > $line.HUMAN; done

ls *intermediate.blast.out.* | paste - - | while read line; do awk '{split(FILENAME,a,"."); print $0 > a[1]"."a[2]".final.blast.out"}' $line; done
for line in $(*intermediate.blast.out.* | paste - -); do awk '{split(FILENAME,a,"."); print $0 > a[1]"."a[2]".final.blast.out"}' $line; done

ls *.final.blast.out | while read line; do paste -s $line > $line".one_line"; done
for line in *.final.blast.out ; do paste -s $line > "$line".one_line; done

mkdir -p intermediate_results

mv *.blast.out ./intermediate_results/
for i in *.blast.out ; do mv $i ./intermediate_results/ ; done

mv *.blast.out.HBV ./intermediate_results/
mv *.blast.out.HUMAN ./intermediate_results/
for i in *.blast.out.HBV ; do mv $i ./intermediate_results/ ; done
for i in *.blast.out.HUMAN ; do mv $i ./intermediate_results/ ; done

echo -e $LCYAN " Collecting blast human and viral coordinates for each integration breakpoint "$Z
ls | paste - - > list_for_cicle
Expand Down