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Removing space form fasta file header

Could anyone suggest me the easier way (linux command line) to remove space(S) from header of the fasta file?

sequence
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updated by thackl thackl • written by kudzu • kudzu

Hello kudzu!

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PS: 135035
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written by Michael Dondrup Michael Dondrup 
perl -lane "s/\s+//g if /^>/; print " file.fa > newfile.fa
perl -lane "s/\s+/_/g if /^>/; print " file.fa > newfile.fa
perl -lane "s/\s+/./g if /^>/; print " file.fa > newfile.fa
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updated by Ram Ram • written by Shicheng Guo Shicheng Guo

1 answer

This has been answered before: How to remove space in headers of fasta files

Since FASTA should not contain spaces anywhere else than in header, removing all spaces is the easiest/fastest way:

tr -d ' ' <in.fa >out.fa  # remove all spaces
tr ' ' '_' <in.fa >out.fa # replace spaces by _

If you want to change headers only:

sed '/^>/{s/ /_/g}' <in.fa >out.fa 
sed '/^>/{s/ \+/_/}' # replace only first occurance of (multiple) spaces
sed '/^>/{s/\s/_/g}' # \s will also target tabs
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updated by Ram Ram • written by thackl thackl

That was very quick and easy command to remove all spaces. Thank you very much for your quick response thackl (Y)

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updated by Ram Ram • written by kudzu • kudzu

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