remove_gaps.py

import sys

import Oligotyping.lib.fastalib as u

fasta = u.SequenceSource(sys.argv[1])
output = u.FastaOutput(sys.argv[2])

while fasta.next():
    if fasta.pos % 10000 == 0:
        sys.stdout.write('\rreads processed so far: %d' % (fasta.pos))
        sys.stdout.flush()

    output.write_id(fasta.id)
    output.write_seq(fasta.seq.replace('-', ''), split = False)


fasta.close()
print