Empty fasta headers
Hi All,
I want to remove empty fasta headers from the fasta file. I used the commands from this biostar post but they seems to work only for nt sequence file (strange!) and I have file with short aa sequnces, would be helpful if anyone help me with one liner perl or awk or similar. Thanks for any help.
infile.fasta
>Seq_1
CMRPQWSIGSN
>Seq_2
>Seq_3
WSIGSNCMRPQWCMRPQ
Output I want:
>Seq_1
CMRPQWSIGSN
>Seq_3
WSIGSNCMRPQWCMRPQ
1 answer
The biostar post you linked gives a awk command that does the job, even for amino acid sequences:
awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} $2 {print ">"$0}' input.fas > output.fas
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Ram
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Frédéric Mahé
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written
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Frédéric Mahé
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