To do blastp iteratively using terminal script

Question

[sinumolg]

I have one input file containing 200 fasta query sequence. I want to do standalone blast for each fasta sequence separately . I am expecting my outfile of blast should be named its corresponding query fasta header name. How to do it using linux terminal scripts? Can anyone help me

Answer 1

[shenwei356]

Using seqkit split(download, usage)and then blast.

seqkit split -i --id-regexp '(.+)' -o output_dir input_seq.fa

File names would be in format of input_seq.id_cel-let-7 MI0000001.fa, let's delete the prefix input_seq.id_:

cd output_dir; 
rename "input_seq.id_"  ""  *.fa

Answer 2

[Pierre Lindenbaum]

(not tested)

linearize and loop

awk '/^>/ {printf("%s%s\n",(N>0?"\n":""),substr($0,2));N++;next;} {printf("%s",$0);} END {printf("\n");}'  inputfasta   | while read F; do echo ">$F" > tmp.fa ; read S ; echo $S | fold -w 60 >> tmp.fa ; blastn -db my.db -query tmp.fa > $F.blast ; rm tmp.fa; done