Remove line breaks in a FASTA file

Question

I have a fasta file where the sequences are broken up with newlines. I\'d like to remove the newlines. Here\'s an example of my file:

>accession1
ATGGCC         


        

Answer 1

Do not reinvent the wheel. If the goal is simply removing newlines in multi-line fasta file (unwrapping fasta file), use any of the specialized bioinformatics tools, for example seqtk, like so:

seqtk seq -l 0 input_file

Example:

# Create the input for testing:

cat > test_unwrap_in.fa <seq1 with blanks
ACGT ACGT ACGT
>seq2 with newlines
ACGT

ACGT

ACGT

>seq3 without blanks or newlines
ACGTACGTACGT

EOF

# Unwrap lines:

seqtk seq -l 0 test_unwrap_in.fa > test_unwrap_out.fa

cat test_unwrap_out.fa

Output:

>seq1 with blanks
ACGT ACGT ACGT
>seq2 with newlines
ACGTACGTACGT
>seq3 without blanks or newlines
ACGTACGTACGT

To install seqtk, you can use for example conda install seqtk.

SEE ALSO:

seqtk usage:

seqtk seq

Usage:   seqtk seq [options] |

Options: ...
         -l INT    number of residues per line; 0 for 2^32-1 [0]