I wanted to merge every line 2-3 together and keep line 1. Here is the example of my text
>chrX:147147161-147148161
ATGATGGTGATGTACAGATGGGTTTTTGG
TTATCTAATTCATGTGTTGGTCAGATCAA
>chrY:16119725-16120725
CAGCTTTGTTCCGTTGCTGGTGAGGAACT
GACTCCCTGGGTGTAGGACCCTCCGAGCC
What I want it to look like
>chrX:147147161-147148161
ATGATGGTGATGTACAGATGGGTTTTTGGTTATCTAATTCATGTGTTGGTCAGATCAA
>chrY:16119725-16120725
CAGCTTTGTTCCGTTGCTGGTGAGGAACTGACTCCCTGGGTGTAGGACCCTCCGAGCC
I have tried several ways but none has been working so far. Here is what I have been trying to do
> sed '/>$/,/>$/ {//b; N; s/\n//;}' file.txt
This command could not merge my lines. I also tried this before
> paste -d "" - - < txt.file .
This only merge my chr line and the sequence line, which was not what I wanted. Can someone give my some suggestions? Thank you!
>Solution :
Assumptions:
- sequence lines do not contain (trailing) white space
- sequence lines do not end with a
\r(windows/dos line ending) - a sequence spans exactly 2 lines (not 1 line, not 3+ lines)
- NOTE: additional logic can be added to address any invalid assumptions
A couple variations on an awk idea:
awk '
(NR%3)==2 { line2=$0; next }
(NR%3)==0 { print line2 $0; next }
1
' file.txt
####################
awk '
(NR%3)==2 { line2=$0; next }
{ print line2 $0 }
(NR%3)==0 { line2="" }
' file.txt
Both of these generate:
>chrX:147147161-147148161
ATGATGGTGATGTACAGATGGGTTTTTGGTTATCTAATTCATGTGTTGGTCAGATCAA
>chrY:16119725-16120725
CAGCTTTGTTCCGTTGCTGGTGAGGAACTGACTCCCTGGGTGTAGGACCCTCCGAGCC