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Fasta headers column spilt or selection
How to take a specific column in sequence header identifiers of fasta file?
I am having my header such as:
>PGM0100236.1 [Candida] scaffold00238
>PGM0100236.1 [Candida] scaffold00239
>PGM0100236.1 [Candida] scaffold00240
>PGM0100236.1 [Candida] scaffold00241
I would like to take my third column alone i.e scaffold00238 for all the headers in my fasta file. Please give a simple command solution. I am new to bioinfo and linux script.
Thank you.
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Ram
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genomics_buddy •
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genomics_buddy •
2 answers
Edit: Apologies, I thougth OP wanted only the names of the scaffolds. Then a solution could be:
awk '/^>/{$0=">"$NF}1' myfile.fasta > output.fasta
This will get the last field of the fasta headers.
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antmantras •
Yeah, I know it can be written with:
grep ">" myfile.fasta | awk '{print $3}' > output.txt
if one is only looking for the names of the third column. However, I think is easier to understand for someone new to Unix what is going on with that command sequence (by first using cat). Anyways, since that is not what OP wanted, I removed that part.
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antmantras •
That's a good reason to use a cat where it's not required (as the Wiki page says). I also use it when I'm "building" a piped command sequence as I often start out with head file | ... and then go back to the working command and replace head with cat, but here on the forum, you can skip the cat-ing as ultimately, people should learn better ways of using commands and while we don't need to be perl-like in complexity, we can avoid over-simplification as well.
A seqkit answer.
seqkit replace -p ".+(scaffold[0-9]+$)" -r "\$1" file.fasta
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This solution also prints the words
scaffoldlosing all other information.What OP wants.
If your file only contains the headers and not the sequence, another easy solution is
If it does contain the sequence then
This assumes that the delimitator between columns is a tab (\t). If it is an empty space, you need to define the delimitator with a
cut -d " " -f3Neither of these solutions are doing what OP wants as far as I can tell.
OP wants to use a word to modify the header of a multi-fasta file.
palani : Please confirm that you want to change
to
Yes, exactly like that. Thanks for all the response. This is my first time in biostars. I am happy for all the suggestions. Thank you all.
Thank you all for your suggestions, I will try it. I am glad for all your support.