I have a list of Linux commands that I need to repeat up to 670. How can I automate the commands, so I don’t have to do the 670 times. I don’t know how to do all the operations from C1, C2, C3 …. to C670?
#START C1
mkdir C1
cd C1
awk '/Prymnesium_parvum_GenomeV1.0_Contig_1\t/' ../Methy_670.txt | cut -f 2 > IllU_C1.txt
awk '/Prymnesium_parvum_GenomeV1.0_Contig_1\t/' ../TE/TEannotation_Prymnesium_parvum_GenomeV1.0.gff3 | cut -f 4,5 > TE_C1.txt
paste TE_C1.txt IllU_C1.txt> C1.txt
awk -f ../com.awk C1.txt C1.txt > res_C1
wc -l res_C1
wc -l TE_C1.txt
cd ..
###Stop C1
#Start C2
mkdir C2
cd C2
awk '/Prymnesium_parvum_GenomeV1.0_Contig_2\t/' ../Methy_670.txt | cut -f 2 > IllU_C1.txt
awk '/Prymnesium_parvum_GenomeV1.0_Contig_2\t/' ../TE/TEannotation_Prymnesium_parvum_GenomeV1.0.gff3 | cut -f 4,5 > TE_C1.txt
....
>Solution :
Not tested:
#!/bin/bash
for C in {1..670};do
echo START ${C}
mkdir -p ${C} && cd ${C}
awk '/Prymnesium_parvum_GenomeV1.0_Contig_'${C}'\t/' ../Methy_670.txt | cut -f 2 > IllU_${C}.txt
awk '/Prymnesium_parvum_GenomeV1.0_Contig_'${C}'\t/' ../TE/TEannotation_Prymnesium_parvum_GenomeV1.0.gff3 | cut -f 4,5 > TE_${C}.txt
paste TE_${C}.txt IllU_${C}.txt> ${C}.txt
awk -f ../com.awk ${C}.txt ${C}.txt > res_${C}
wc -l res_${C}
wc -l TE_${C}.txt
cd ..
echo Stop ${C}
done
I am not sure what awk '/Prymnesium_parvum_GenomeV1.0_Contig_1\t/' ../Methy_670.txt does but you will have to figure out how you can add ${C} in there as single quotes will not parse ${C}