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Append file name to fasta file headers in Linux

 
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# 1  
Old 01-03-2014
Append file name to fasta file headers in Linux
How do we append the file name to fasta file headers in multiple fasta-files in Linux?
Last edited by Mauve; 01-05-2014 at 02:36 PM..
# 2  
Old 01-03-2014
Using awk:
Code:
awk 'NR==1{$0=$0"|"FILENAME}1' file.fasta

# 3  
Old 01-05-2014
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?
Last edited by Mauve; 01-05-2014 at 02:18 PM..
# 4  
Old 01-05-2014
Post sample input and expected output in code tags
# 5  
Old 01-05-2014
I did, but it was removed.. here goes again: fasta files (e.g. sample_1.fasta) in format:
Code:
>node_1
atgatgatgat
>node_3
gtcgtcgtcgtcgtc
>node_12
gtagtagta

Expected output:
Code:
>sample_1_node_1
atgatgatgat
>sample_1_node_3
gtcgtcgtcgtcgtc
>sample_1_node_12
gtagtagta

# 6  
Old 01-05-2014
Code:
awk '/>/{sub(">","&"FILENAME"_");sub(/\.fasta/,x)}1' sample_1.fasta

This User Gave Thanks to Yoda For This Post:
Mauve
# 7  
Old 01-05-2014
Brilliant, thank you! Smilie
 
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