linearize the fasta

filter with awk and a regular expression, convert back to fasta

awk -f linearizefasta.awk < input.fa | awk -F '\t' '($2 ~ /N/)' | tr "\t" "\n"

With one-line fasta and with sequence names specifically 'seq#' (i.e. no letter 'N's), you can super easily do:

grep -B 1 'N' input.fasta >output_no_Ns.fasta

But that is assuming your data is in the specific format above. Multi line fasta or N's in your headers would break it. But this is what I'd do if I had this data.

Hi,

First, I linearized multi-line fasta file to single-line fasta file:

Multiline Fasta To Single Line Fasta

awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' < file.fa

Than, @Daniel command:

grep -B 1 'N' input.fasta >output_no_Ns.fasta

I apologized the community for not explaining my question properly.

Best,
Waqas.

In Python, for a file named foo.fa containing linearised FASTAs (prunes FASTAs with Ns):

header = ''

for line in open('foo.fa'):
    if '>' in line:
        header = line
    elif line == '\n':
        pass
    elif 'N' not in line.upper():
        print header,
        print line,

With the BBMap package:

reformat.sh in=file.fasta out=fixed.fasta maxns=0