我如何在 fasta 文件中输入 grep 模式，然后将所有这些对应序列打印到 fasta 文件中？

Question

I've had so much help with code errors when I've used this page. I really appreciate how much everyone wants to help out.!! I am brand new to any kind of coding and whooooooh this is a learning curve.

Anyways, I am trying to use the grep command to search for matching sequences from a list of patterns that are in my patterns.txt file. I am trying to take those sequences, and write a new.fasta file for each one and put them into a new directory. I am trying to do this all in bash.

This is the bash script I wrote, but I'm not getting any output at all (except the directory gets made which is not that useful)

Edit**** for clarity: my question is I need to crease a FASTA file for each pattern that contains all the genes and their corresponding sequences that have that pattern. I want to name each file after the pattern and output it into a new directory. Ithink my original question was a little confusing!

mkdir SEQUENCE-MATCHES



for pattern; do
        grep -B1 $pattern my_file.fasta
done < patterns_file.txt > SEQUENCE-MATCHES/$pattern.fasta

This isn't outputting anything at all. I could manually run grep on all of the patterns, but it's too long to be realistic.

Answer 1

for pattern; do for pattern; do doesn't set pattern the way you want.

Also, you merged all the output into a single file.

Try:

while read pattern; do
    grep -B1 "$pattern" my_file.fasta > SEQUENCE-MATCHES/"$pattern".fasta
done < pattern_file.txt

Note that this code also creates an empty output file for each pattern that doesn't match.