how to merge lines that do not begin with certain character

Question

if i have the following:

>A13P0
ACCATAGAGAG
CCCGAGATTTA
>03HK2
ACACAGTGTGT
TTAGAGGGAGA

How do I merge lines that do not begin with >?

i.e.

>A13P0
ACCATAGAGAGCCCGAGATTTA
>03HK2
ACACAGTGTGTTTAGAGGGAGA

thanks!

ikegami · Accepted Answer · 2017-06-27T18:29:36.643

4

perl -ne'
   if (/^>/) {
      print("\n") if $. != 1;
   } else {
      chomp;
   }
   print;
} {
   print("\n") if $. != 1;
'

edited Jun 27 '17 at 18:29

answered May 30 '16 at 14:55

ikegami

Maybe you should precise that this is Perl. – Aif May 30 '16 at 14:58
@Ed Morton, Replacing `chomp;` with `s/\s+\z//;` will cause it accept both CRLF and LF. – ikegami May 30 '16 at 15:16

score 2 · Answer 2 · answered May 30 '16 at 15:02

2

I know this has been asked/answered a thousand times but I can't find it so:

$ awk '/^>/{print (NR>1?ORS:"") $0; next} {printf "%s", $0} END{print ""}' file
>A13P0
ACCATAGAGAGCCCGAGATTTA
>03HK2
ACACAGTGTGTTTAGAGGGAGA

answered May 30 '16 at 15:02

Ed Morton

score 2 · Answer 3 · answered May 30 '16 at 15:51

2

with a perl command line:

perl -pE '$.>1 && !s/^>/\n>/ && chomp; END{say}' file

answered May 30 '16 at 15:51

SLePort · Answer 4 · 2016-05-30T18:22:46.350

0

With sed :

$ sed ':a;$!N;/>/!{s/\n\([^>]\)/\1/;ta};P;D' file
>A13P0
ACCATAGAGAGCCCGAGATTTA
>03HK2
ACACAGTGTGTTTAGAGGGAGA

edited May 30 '16 at 18:22

answered May 30 '16 at 16:15

SLePort

4 Answers4