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

There have been great responses so far.

Here is an efficient way to do this in Python:

def read_fasta(fasta):
    with open(fasta, 'r') as fast:
        headers, sequences = [], []
        for line in fast:
            if line.startswith('>'):
                head = line.replace('>','').strip()
                headers.append(head)
                sequences.append('')
            else :
                seq = line.strip()
                if len(seq) > 0:
                    sequences[-1] += seq
    return (headers, sequences)


def write_fasta(headers, sequences, fasta):
    with open(fasta, 'w') as fast:
        for i in range(len(headers)):
            fast.write('>' + headers[i] + '\n' + sequences[i] + '\n')

You can use the above functions to retrieve sequences/headers from a fasta file without line breaks, manipulate them, and write back to a fasta file.

headers, sequences = read_fasta('input.fasta')
new_headers = do_something(headers)
new_sequences = do_something(sequences)
write_fasta(new_headers, new_sequences, 'input.fasta')