def print_fastq(fc, fq): pairs = izip(fc, fq) while True: try: seq_header, qual_header = pairs.next() except StopIteration: break assert seq_header == qual_header, (seq_header, qual_header) assert seq_header[0] == ">" cs, qual = pairs.next() qual = qual.strip().split(" ") print "@%s" % seq_header[1:].strip() print cs2seq(cs.strip()) print "+" # since the qual is 1 short, just add an extra here to the end. print "".join(chr(int(q) + 33) for q in qual) + chr(int(qual[-1]) + 33)
def print_fasta(fc): header = fc.readline() while header: print header, print cs2seq(fc.readline().strip()) header = fc.readline()