Hello.

How to extract a protein sequence?

I have two files.

< file 1. complete_protein.fasta > 

>protein_1

>DCXSTEISLFHEIWLF

>protein_2

>AJFOWIDJLSIDJFJ

>protein_3

>DJFLWIDJFLSKDJFL

>protein_4

>DKSJFLEISJDKJF

< file 2. only proteinID.fasta >

>protein_1

>protein_4

I need about sequence in file2. That sequence have in file1.

So, I tried "diff" command, but result is I don't want data.

How to extract??



Hi, 

If you are working with linux distribution you can try the following command-line: 

    grep -f target_protein.txt -A1 protein_file.txt | sed '/--/d'  > retrieved_protein.txt

This takes the `protein_file.txt` file that contains the same content that you posted above: 

> 
    protein_1
    DCXSTEISLFHEIWLF
    protein_2
    AJFOWIDJLSIDJFJ
    protein_3  
    DJFLWIDJFLSKDJFL
    protein_4
    DKSJFLEISJDKJF

And the file `target_protein.txt` that contains the target protein names that you want to retrieve from the file above: 

> 
    protein_1
    protein_4

The output of protein target sequences of interest is saved in `retrieved_protein.txt`, that looks like:

> 
    protein_1
    DCXSTEISLFHEIWLF
    protein_4
    DKSJFLEISJDKJF

I hope this helps, 

António

 
