Useage.sh

#Make sure you have installed

for i in *.fa;do
name=${i%.fa}
blastn -task blastn-short -query ./${name}.fa -subject ./attL.fa -out ./mapping/${name}.txt -num_threads 1 -outfmt 7 -evalue 1.0e-4 &
done
#Clean reads were mapped to ATTL reconbination sequence in FASTA format to locate the ATTL position in the reads and split the reads.
#Make sure the ATTL reads in FASTA format is in current directory.

python3 PPI_Finder1.py ./mapping/${name}.txt ./${name}.fa ./split/${name}
#Using the python3 script to split the Pacbio 3rd sequencing reads into different file in FASTA format.
#PPI_Finder1.py is avaiable as https://github.com/yannnnLi/Highthrough-put-Y2H-analysis_NewVersion.

makeblastdb -in ../cds/B73_CDS.fa -dbtype nucl -out ../cds/B73 -parse_seqids
#Construct index of sequence alignment
for i in lib*_1.fa
do
name=${i%_*}
blastn -db ../cds/B73 -query ${name}_1.fa -out ${name}_1.txt -evalue 1.0e-4 -num_threads 1 -outfmt 6 -max_target_seqs 1 &
blastn -db ../cds/B73 -query ${name}_2.fa -out ${name}_2.txt -evalue 1.0e-4 -num_threads 1 -outfmt 6 -max_target_seqs 1 &
blastn -task blastn-short -query ${name}_1.fa -subject primer.fa -out ${name}_1_primer.txt -num_threads 1 -outfmt 6 -max_target_seqs 1 -evalue 1.0e-4 &
blastn -task blastn-short -query ${name}_2.fa -subject primer.fa -out ${name}_2_primer.txt -num_threads 1 -outfmt 6 -max_target_seqs 1 -evalue 1.0e-4 &
done
#Split reads were mapped to reference CDS sequence.
#Make sure the primer(AD,BD) reads in FASTA format is in current directory.

for i in libB73*_1.txt
do
name=${i%_*}
python3 PPI_Finder2.py ${name}_1.txt ${name}_1_primer.txt ${name}_2.txt ${name}_2_primer.txt > ${name}_result.txt &
done
#Parsing the mapping result to find protein-protein interactions using python3 script.
PPI_Finder2.py is avaiable at https://github.com/yannnnLi/Highthrough-put-Y2H-analysis_NewVersion.