Append file name to fasta file headers in Linux

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1

How do we append the file name to fasta file headers in multiple fasta-files in Linux?

2

Using awk:

awk 'NR==1{$0=$0"|"FILENAME}1' file.fasta
3

Gave awk a try, but this appears to print the filename in the first header only, not to change it in place, and also this does not affect the subsequent headers. Any alternative solutions?

4

Post sample input and expected output in code tags

5

I did, but it was removed.. here goes again: fasta files (e.g. sample_1.fasta) in format:

>node_1
atgatgatgat
>node_3
gtcgtcgtcgtcgtc
>node_12
gtagtagta

Expected output:

>sample_1_node_1
atgatgatgat
>sample_1_node_3
gtcgtcgtcgtcgtc
>sample_1_node_12
gtagtagta
6 
awk '/>/{sub(">","&"FILENAME"_");sub(/\.fasta/,x)}1' sample_1.fasta
7

Brilliant, thank you! :b:

8

Is it also possible to modify this code, for example using a for-loop, to perform this action on all .fasta files in a directory (outputing the modified files to a new directory or similarly)?

9 
for file in /source_dir/*.fasta
do
        fname="${file##*/}"
        awk '/>/{sub(">","&"FILENAME"_");sub(/\.fasta/,x)}1' "$file" > /dest_dir/$fname"
done
10 
for file in /source_dir/*.fasta
do
        fname="${file##*/}"
        awk '/>/{sub(">","&"FILENAME"_");sub(/\.fasta/,x)}1' "$file" > /dest_dir/$fname"
done
11

OR this

$ awk '/>/{sub(/\..*/,x,FILENAME);$0=FILENAME"_"$2}1' FS=">" sample_1.fasta 

sample_1_node_1
atgatgatgat
sample_1_node_3
gtcgtcgtcgtcgtc
sample_1_node_12
gtagtagta