Quick functions for reading and writing fastq files.

read_write_fastq

"""Quick functions for reading and writing FASTQ"""

def read_fastq(filehandle):
    ''' Return dictionary with 'seq_id', 'seq', 'qual_id', and 'qual'  '''
    record_line = 0
    read_number = 0
    fastq_record = dict()
    for line in filehandle:
        record_line += 1
        if record_line == 1:
            fastq_record['seq_id'] = line.strip()
        elif record_line == 2:
            fastq_record['seq'] = line.strip()
        elif record_line == 3:
            fastq_record['qual_id'] = line.strip()
        elif record_line == 4:
            record_line = 0
            fastq_record['qual'] = line.strip()
            read_number += 1
            yield fastq_record

def fastq_string(record):
    return "%s\n%s\n%s\n%s\n" % (record['seq_id'], record['seq'], record['qual_id'], record['qual'])