Move new line character 5 positions downstream in a text (fasta) file - awk

Question

I am trying to transform a text file like this (fasta format):
>seq1
AAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAA
ATGATGATGGAATGAGGAT
TTAGGAGGGAGGAAAATTC
>seq2
CCCTCCGGGAAAAAAGAGG
TTGCAATGCGCGTATTTAT
TTTTTTTTTTTTTTTTTTT
AAAAAAAAAAAAAGGCTGT
AAAAAAAAAAAAAAAGGGG
The objective is to displace newline character 5 positions downstream, except for those lines starting with >
>seq1
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAATGATGATGGAATGA
GGATTTAGGAGGGAGGAAAATTC
>seq2
CCCTCCGGGAAAAAAGAGGTTGCA
ATGCGCGTATTTATTTTTTTTTTT
TTTTTTTTTAAAAAAAAAAAAAGG
CTGTAAAAAAAAAAAAAAAGGGG
I would like to use AWK, but I am not sure how to proceed. I am thinking about something similar to this:
awk '{for(i=1;i<=NR;i++){ if($1 ~ /^>/){¿?¿?¿?}}}'
Do you know how can I solve this?

Answer 1

Assumptions:
all data lines are to be expanded to a max of 24 characters
One awk idea:
awk -v width=24 ' # pass width in as awk variable "width"
function print_sequence() {
if (sequence) # if sequence is not blank
while (sequence) { # while sequence is not blank
print substr(sequence,1,width) # print 1st 24 characters
sequence=substr(sequence,width+1) # remove 1st 24 characters
}
}
/^>/ { print_sequence() # flush previous set of data to stdout
print # print current input line
next # process next input line
}
{ sequence=sequence $1 } # append data to our "sequence" variable
END { print_sequence() } # flush last set of data to stdout
' fasta.in > fasta.out
This generates:
$ cat fasta.out
>seq1
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAATGATGATGGAATGA
GGATTTAGGAGGGAGGAAAATTC
>seq2
CCCTCCGGGAAAAAAGAGGTTGCA
ATGCGCGTATTTATTTTTTTTTTT
TTTTTTTTTAAAAAAAAAAAAAGG
CTGTAAAAAAAAAAAAAAAGGGG

Answer 2

I would do it following way, let file.txt content be
>seq1
AAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAA
ATGATGATGGAATGAGGAT
TTAGGAGGGAGGAAAATTC
>seq2
CCCTCCGGGAAAAAAGAGG
TTGCAATGCGCGTATTTAT
TTTTTTTTTTTTTTTTTTT
AAAAAAAAAAAAAGGCTGT
AAAAAAAAAAAAAAAGGGG
then
awk 'BEGIN{width=24}/>/&&x{print x;x=""}/>/{print;next}{x = x $0}length(x)>=width{print substr(x,1,width);x=substr(x,width+1)}END{print x}' file.txt
gives output
>seq1
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAATGATGATGGAATGA
GGATTTAGGAGGGAGGAAAATTC
>seq2
CCCTCCGGGAAAAAAGAGGTTGCA
ATGCGCGTATTTATTTTTTTTTTT
TTTTTTTTTAAAAAAAAAAAAAGG
CTGTAAAAAAAAAAAAAAAGGGG
Explanation: I set width to 24 which is number of desired character, if > is found and there is something stored in x do print that and set x value to empty string, if line with > is encountered do print it and go to next line. For every line do append current line content to x, if length of x is equal to or greater than width do print width first characters of x and remove these characters from x. After processing all lines do print x. Disclaimer solution: this solution assumes that ratio between current width and desired with is lesser than 0.5
(GNU Awk 5.0.1)

Answer 3

Yet another approach you could try, using awk's field and record separators:
awk -v width=24 '
BEGIN {
FS="\n" # Set the Field separator to newline
RS=">" # Set the Record separator to ">"
ORS=OFS="" # Set the Output Record and Field separator to an empty string
}
NR>1 { # Using ">" as a record separator the first record is empty, so skip
header=$1 # Using "\n" as the Field separator, $1 contains the header, save it in a variable
$1=OFS # Assign an empty string to $1 so the record gets recalculated and the body becomes $0 i
# with all newlines are removed, since OFS == ""
gsub(".{" width "}", "&" FS) # Append every "width" characters with a newline (FS)
print RS header FS $0 FS # Print a ">", the header, a newline, the body and a newline
}
' fasta_in > fasta_out

Answer 4

Assuming the line that starts with > is never more than 24 chars long:
$ awk '{printf "%s", (/^>/ ? sep $0 ORS : $0); sep=ORS} END{print ""}' file | fold -w24
>seq1
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAATGATGATGGAATGA
GGATTTAGGAGGGAGGAAAATTC
>seq2
CCCTCCGGGAAAAAAGAGGTTGCA
ATGCGCGTATTTATTTTTTTTTTT
TTTTTTTTTAAAAAAAAAAAAAGG
CTGTAAAAAAAAAAAAAAAGGGG