MY SCRIPT (12):Position analysis of any gene by BLAST and manipulation ........

#Used this pipeline to find position of some transposases of M. tuberculosis H37Rv
#BLAST
#! usr/bin/bash
#Protein BLAST
#execute as sh Rv_gene_manipulation.sh |&  tee Rv_data
#Its comparing only with H37Rv
#mkdir /home/pseema/denovo_analysis/result_files/Rv_results
mkdir /home/pseema/denovo_analysis/genome_fasta_files
#! usr/bin/bash
while read isolate;
do
echo "Starting the $isolate genome"
awk '/>/{sub(">","&"FILENAME"_");sub(/\.fasta/,x)}1' /home/pseema/denovo_analysis/gene_fasta_files/$isolate.fasta  > /home/pseema/denovo_analysis/genome_fasta_files/$isolate.fasta
done < /home/pseema/denovo_analysis/input_files/isolate_list
while read isolate;
do
echo "Starting the $isolate"
echo "###################################################"
blastn -query  /home/pseema/denovo_analysis/Rv_genes/Rv0920c.fasta -subject /home/pseema/denovo_analysis/genome_fasta_files/$isolate.fasta   > /home/pseema/denovo_analysis/result_files/Rv_results/result_Rv0920c.fasta
echo "Total number of Rv0920c hits for $isolate"
grep 'Strand' /home/pseema/denovo_analysis/result_files/Rv_results/result_Rv0920c.fasta | wc
echo "Copies in plus strand"
grep 'Strand=Plus/Plus' /home/pseema/denovo_analysis/result_files/Rv_results/result_Rv0920c.fasta | wc
echo "Copies in minus strand"
grep 'Strand=Plus/Minus' /home/pseema/denovo_analysis/result_files/Rv_results/result_Rv0920c.fasta | wc

echo "###################################################"
blastn -query  /home/pseema/denovo_analysis/Rv_genes/Rv0921.fasta -subject /home/pseema/denovo_analysis/genome_fasta_files/$isolate.fasta   > /home/pseema/denovo_analysis/result_files/Rv_results/result_Rv0921.fasta
echo "Total number of Rv0921 hits for $isolate"
echo "Copies in plus strand"
grep 'Strand=Plus/Plus' /home/pseema/denovo_analysis/result_files/Rv_results/result_Rv0921.fasta | wc
echo "Copies in minus strand"
grep 'Strand=Plus/Minus' /home/pseema/denovo_analysis/result_files/Rv_results/result_Rv0921.fasta | wc

echo "###################################################"
blastn -query  /home/pseema/denovo_analysis/Rv_genes/Rv0922.fasta -subject /home/pseema/denovo_analysis/genome_fasta_files/$isolate.fasta   > /home/pseema/denovo_analysis/result_files/Rv_results/result_Rv0922.fasta
echo "Total number of Rv0922 hits for $isolate"
echo "Copies in plus strand"
grep 'Strand=Plus/Plus' /home/pseema/denovo_analysis/result_files/Rv_results/result_Rv0922.fasta | wc
echo "Copies in minus strand"
grep 'Strand=Plus/Minus' /home/pseema/denovo_analysis/result_files/Rv_results/result_Rv0922.fasta | wc

done < /home/pseema/denovo_analysis/input_files/isolate_list
#Homology
#! usr/bin/bash
#execute as sh Rv_gene_homology.sh

while read isolate;
do
blastn -query  /home/pseema/denovo_analysis/Rv_genes/Rv0920c.fasta -subject /home/pseema/denovo_analysis/genome_fasta_files/$isolate.fasta  
done < /home/pseema/denovo_analysis/input_files/isolate_list |& tee /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c.blast_result

while read isolate;
do
blastn -query  /home/pseema/denovo_analysis/Rv_genes/Rv0921.fasta -subject /home/pseema/denovo_analysis/genome_fasta_files/$isolate.fasta  
done < /home/pseema/denovo_analysis/input_files/isolate_list |& tee /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921.blast_result

while read isolate;
do
blastn -query  /home/pseema/denovo_analysis/Rv_genes/Rv0922.fasta -subject /home/pseema/denovo_analysis/genome_fasta_files/$isolate.fasta 
done < /home/pseema/denovo_analysis/input_files/isolate_list |& tee /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922.blast_result

#Analysis
#! usr/bin/bash
#sh Rv_gene_analysis.sh |& tee Rv_pos_file
echo "***********Matches of Rv0920c  at the start of alignment**********"
grep  "TCAGCGTTCTTCGGCGGCTGGCATGCGATCGGCGAACGTGATCGCCAGGGCGTTGAGCGC" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c.blast_result  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_position
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_position |wc -l
#Extract lines with the pattern '/Sbjct/'
awk '/Sbjct/' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_position > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_only_subj_start
#Extract field 2 of the file
awk '{print $2}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_only_subj_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_column_2

echo "Total Rv0920c  copies :"
awk '{print $2, $4}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_only_subj_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4 |wc -l


echo "Rv0920c  in plus strand :"
awk '$2 > $1 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_plus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_plus |wc -l
#############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_plus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_plus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_plus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_plus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_plus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_start
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_start
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_start
##############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_start
#The file Rv0920c_plus_trimmed_sorted_start will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_start

echo "Rv0920c  in minus strand :"
awk '$1 > $2 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_minus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_minus |wc -l
#############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_minus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_minus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_minus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_minus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_minus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_start
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_start_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_start
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_start
##############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_start
#The file Rv0920c_minus_trimmed_sorted_start will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_start

echo "***********Matches of Rv0920c  at the end of alignment**********"
grep  "GGCCGCCTCATCCACGTCCTGGCCGGCGTGAGCCGGCTCTATCACCTGAGCAGCATCCAT" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c.blast_result  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_position
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_position |wc -l
awk '/Sbjct/' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_position > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_only_subj_end
#Extract field 4 of the file
awk '{print $4}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_only_subj_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_column_4

echo "Total Rv0920c  copies :"
awk '{print $2, $4}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_only_subj_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4 |wc -l
echo "Rv0920c  in plus strand :"
awk '$2 > $1 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_plus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_plus |wc -l
##############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_plus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_plus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_plus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_plus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_plus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_end
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_end
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_end
#############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_end
#The file Rv0920c_plus_trimmed_sorted_end will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_end

echo "Rv0920c  in minus strand :"
awk '$1 > $2 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_minus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_minus |wc -l
##############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_minus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_minus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_minus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_minus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_minus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_end
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_end_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_end
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_end
#############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_end
#The file Rv0920c_minus_trimmed_sorted_end will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_end

grep -q "Identities =" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c.blast_result
#grep "Identities =" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c.blast_result |wc -l
echo "Total number of Rv0920c  copies across the isolates"
grep "Strand=" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c.blast_result |wc -l
echo "Copies in plus and minus strand"
grep "Strand=Plus/Plus" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c.blast_result |wc -l
grep "Strand=Plus/Minus" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c.blast_result |wc -l

echo "*********************Rv0920c  analysis done*******************"

echo "***********Matches of Rv0921  at the start of alignment**********"
grep  "GTGAATCTGGCGGATTGGGCGGAGTCGGTGGGGGTGAATCGACATACCGCTTATCGCTGG" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921.blast_result  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_position
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_position |wc -l
#Extract lines with the pattern '/Sbjct/'
awk '/Sbjct/' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_position > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_only_subj_start
#Extract field 2 of the file
awk '{print $2}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_only_subj_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_column_2

echo "Total Rv0921  copies :"
awk '{print $2, $4}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_only_subj_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4 |wc -l


echo "Rv0921  in plus strand :"
awk '$2 > $1 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_plus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_plus |wc -l
#############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_plus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_plus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_plus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_plus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_plus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_start
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_start
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_start
##############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_start
#The file Rv0921_plus_trimmed_sorted_start will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_start

echo "Rv0921  in minus strand :"
awk '$1 > $2 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_minus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_minus |wc -l
#############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_minus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_minus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_minus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_minus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_minus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_start
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_start_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_start
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_start
##############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_start
#The file Rv0921_minus_trimmed_sorted_start will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_start

echo "***********Matches of Rv0921  at the end of alignment**********"
grep  "CGTGCGGTCACGGAGGCCAAGCGTGAGCCGGGGGCGGGGTGA" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921.blast_result  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_position
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_position |wc -l
awk '/Sbjct/' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_position > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_only_subj_end
#Extract field 4 of the file
awk '{print $4}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_only_subj_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_column_4

echo "Total Rv0921  copies :"
awk '{print $2, $4}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_only_subj_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4 |wc -l
echo "Rv0921  in plus strand :"
awk '$2 > $1 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_plus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_plus |wc -l
##############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_plus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_plus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_plus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_plus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_plus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_end
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_end
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_end
#############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_end
#The file Rv0921_plus_trimmed_sorted_end will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_end

echo "Rv0921  in minus strand :"
awk '$1 > $2 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_minus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_minus |wc -l
##############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_minus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_minus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_minus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_minus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_minus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_end
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_end_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_end
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_end
#############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_end
#The file Rv0921_minus_trimmed_sorted_end will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_end

grep -q "Identities =" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921.blast_result
#grep "Identities =" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921.blast_result |wc -l
echo "Total number of Rv0921  copies across the isolates"
grep "Strand=" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921.blast_result |wc -l
echo "Copies in plus and minus strand"
grep "Strand=Plus/Plus" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921.blast_result |wc -l
grep "Strand=Plus/Minus" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921.blast_result |wc -l

echo "*********************Rv0921  analysis done*******************"

echo "***********Matches of Rv0922  at the start of alignment**********"
grep  "ATGATCGTCAGGATGCGTAGCTGCGCTCAGGCCGCGAAGGTGGCCGAGGCCACCGGTGGT" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922.blast_result  > /home/pseema/denovo_analysis/result_files/Rv_resultsRv0922_start_position
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_position |wc -l
#Extract lines with the pattern '/Sbjct/'
awk '/Sbjct/' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_position > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_only_subj_start
#Extract field 2 of the file
awk '{print $2}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_only_subj_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_column_2

echo "Total Rv0922  copies :"
awk '{print $2, $4}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_only_subj_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4 |wc -l


echo "Rv0922  in plus strand :"
awk '$2 > $1 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_plus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_plus |wc -l
#############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_plus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_plus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_plus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_plus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_plus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_start
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_start
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_start
##############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_start
#The file Rv0922_plus_trimmed_sorted_start will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_start

echo "Rv0922  in minus strand :"
awk '$1 > $2 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_minus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_minus |wc -l
#############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_minus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_minus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_minus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_minus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_minus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_start
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_start_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_start
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_start
##############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_start > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_start
#The file Rv0922_minus_trimmed_sorted_start will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_start

echo "***********Matches of Rv0922  at the end of alignment**********"
grep  "AAAACCCAAACCCCGCAAGGGGACGCCGCATGA" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922.blast_result  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_position
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_position |wc -l
awk '/Sbjct/' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_position > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_only_subj_end
#Extract field 4 of the file
awk '{print $4}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_only_subj_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_column_4

echo "Total Rv0922  copies :"
awk '{print $2, $4}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_only_subj_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4 |wc -l
echo "Rv0922  in plus strand :"
awk '$2 > $1 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_plus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_plus |wc -l
##############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_plus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_plus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_plus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_plus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_plus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_end
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_plus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_end
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_end
#############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_end
#The file Rv0922_plus_trimmed_sorted_end will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_end

echo "Rv0922  in minus strand :"
awk '$1 > $2 {print $0}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4 > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_minus
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_minus |wc -l
##############
awk '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_minus  > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_minus_mod && mv /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_minus_mod /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_minus

cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_minus
#cut -c 1-4  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_end
sed -e 's/...$//'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_end_column_2_4_minus > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_end
cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_end
#############
sort -n /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_end > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_end
#The file Rv0922_minus_trimmed_sorted_end will give the hotspots of the IS element occurring
#cat /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_end

grep -q "Identities =" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922.blast_result
#grep "Identities =" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922.blast_result |wc -l
echo "Total number of Rv0922  copies across the isolates"
grep "Strand=" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922.blast_result |wc -l
echo "Copies in plus and minus strand"
grep "Strand=Plus/Plus" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922.blast_result |wc -l
grep "Strand=Plus/Minus" /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922.blast_result |wc -l

echo "*********************Rv0922  analysis done*******************"




echo "*********************Rv0920c starting**********************"
echo "#######All plus start positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_start | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_start | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_start_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_start | sort | uniq -c | sort -nr

echo "#######All plus end positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_end | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_end | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_end_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_end  | sort | uniq -c | sort -nr

echo "#######All minus start positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_start | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_start | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_start_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_start | sort | uniq -c | sort -nr

echo "#######All plus end positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_end | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_end | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_end_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_end  | sort | uniq -c | sort -nr

awk '{print $1}'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_start_unique /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_plus_trimmed_sorted_end_unique  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_start_unique /home/pseema/denovo_analysis/result_files/Rv_results/Rv0920c_minus_trimmed_sorted_end_unique > /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0920c
echo "combined_Rv0920c"
echo "sorted"
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0920c | sort
echo "sorted unique"
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0920c | sort | uniq -c
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0920c | sort | uniq -c | wc -l
echo "sorted unique sorted"
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0920c | sort | uniq -c | sort -nr

echo "********************Rv0920c done***************************"

echo "*********************Rv0921 starting**********************"
echo "#######All plus start positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_start | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_start | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_start_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_start | sort | uniq -c | sort -nr

echo "#######All plus end positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_end | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_end | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_end_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_end  | sort | uniq -c | sort -nr

echo "#######All minus start positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_start | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_start | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_start_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_start | sort | uniq -c | sort -nr

echo "#######All plus end positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_end | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_end | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_end_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_end  | sort | uniq -c | sort -nr

awk '{print $1}'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_start_unique /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_plus_trimmed_sorted_end_unique  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_start_unique /home/pseema/denovo_analysis/result_files/Rv_results/Rv0921_minus_trimmed_sorted_end_unique > /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0921
echo "combined_Rv0921"
echo "sorted"
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0921 | sort
echo "sorted unique"
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0921 | sort | uniq -c
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0921 | sort | uniq -c | wc -l
echo "sorted unique sorted"
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0921 | sort | uniq -c | sort -nr

echo "********************Rv0921 done***************************"


echo "*********************Rv0922 starting**********************"
echo "#######All plus start positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_start | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_start | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_start_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_start | sort | uniq -c | sort -nr

echo "#######All plus end positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_end | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_end | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_end_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_end  | sort | uniq -c | sort -nr

echo "#######All minus start positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_start | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_start | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_start_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_start | sort | uniq -c | sort -nr

echo "#######All plus end positions#######"
echo "No. of unique positions"
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_end | sort -n |uniq |wc -l
cat  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_end | sort -n |uniq > /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_end_unique
echo "Positions with highest frequency"
awk -F '\t' '{print $1}' /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_end  | sort | uniq -c | sort -nr

awk '{print $1}'  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_start_unique /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_plus_trimmed_sorted_end_unique  /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_start_unique /home/pseema/denovo_analysis/result_files/Rv_results/Rv0922_minus_trimmed_sorted_end_unique > /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0922
echo "combined_Rv0922"
echo "sorted"
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0922 | sort
echo "sorted unique"
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0922 | sort | uniq -c
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0922 | sort | uniq -c | wc -l
echo "sorted unique sorted"
cat /home/pseema/denovo_analysis/result_files/Rv_results/combined_Rv0922 | sort | uniq -c | sort -nr

echo "********************Rv0922 done***************************"