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loopsunixblast

How can i loop through all my .fasta files?

I wrote a code to go through all my .fasta files in my directory but it is not working. I want it to match with my -db Viral.fna and output (fasta file name).txt and -outfmt 6

I tried 2 different codes

for f in file1.fasta file2.fasta etc ...
do blastn -db Viral.fna -query $f.fasta  -out $f_output3.txt -outfmt 6
Done

Which didn't work: gave me this error 

Command line argument error: Argument "query". File is not accessible:  `file1.fasta.fasta'and repeated for all the files

I also tried this :

for f in 'ls *.fasta' 
do  blastn -db Viral.fna -query $f  -out $f_output3.txt -outfmt 6
Done

Can someone help me out with figure out how to make this loop work I keep getting an error that says 

Too many positional arguments (1), the offending value: 123.fasta
Solution

  • The .fasta extension is already part of $f, so don't add it. And if there's whitespace in any of the file names you have to use quotes where you use $f:

    -query "$f" -out "$f"_output3.txt

    Also, when you write $f_output3.txt, the shell will think you want use a variable called f_output3 which doesn't exist