Joining Line Breaks in FASTA file With Condition in SED/AWK/Perl one-liner

I have a data that looks like this

> sq1
foofoofoobar
foofoofoo
> sq2
quxquxquxbar
quxquxquxbar
quxx
> sq3
paxpaxpax
pax

What I want to do is to join them into one lines:

> sq1 foofoofoobarfoofoofoo
> sq2 quxquxquxbarquxquxquxbarquxx
> sq3 paxpaxpaxpax

I tried this code but fail.

sed -e 'te' -e 'H;$!d;:e' -e 'x;/^$/d开发者_JAVA技巧;s/\n//g'

What's the right way to do it?

$ awk '/^>/&&NR>1{print "";}{ printf "%s",/^>/ ? $0" ":$0 }' file 
> sq1 foofoofoobarfoofoofoo
> sq2 quxquxquxbarquxquxquxbarquxx
> sq3 paxpaxpaxpax

This is one way to do what you want using sed:

sed -n '1{x;d;x};${H;x;s/\n/ /1;s/\n//g;p;b};/^>/{x;s/\n/ /1;s/\n//g;p;b};H'

perl -ne '!/^>/ ? chomp($p) : (chomp $_, $_.=" "); print $p; $p = $_; END{print $p}

... which, of course, could be written a lot shorter if desired.

This is might work for you:

sed ':a;$!{N;ba};s/\n//g;s/> sq[0-9]*/\n& /g;s/.//' file

or this:

 sed ':a;$!N;s/\n\([^>]\)/\a\1/;ta;s/\a/ /;s///g;P;D' file

or this:

 awk -vRS='> sq' '{sub(/^/,RS);sub(/\n/," ");gsub(/\n/,"")};NR>1' file

Shortest sed solution what I was able to find:

sed -n '/^>/!{H;$!b};s/$/ /;x;1b;s/\n//g;p'