Esempio n. 1
0
def print_sequences(args):
    db = sqlite3.connect(args.dbname)
    sql = fetch_reads
    if args.limit is not None:
        sql += ' LIMIT {}'.format(args.limit)
    for defline, blob in db.execute(sql).fetchall():
        x = FASTQ(blob)
        # x._def = "{}".format(rid)
        x._def = defline 
        x.unpack()
        print(x)
Esempio n. 2
0
#

from FASTQ import *


def print_info(seq):
    print()
    print('defline:  ', seq.defline())
    print('sequence: ', seq.sequence())
    print('quality:  ', seq.quality())
    print('blob:     ', seq.blob())


# Create a FASTQ object from a string

seq1 = FASTQ('@NS500451\nNCAAGNGCCA\n+\n#AAAA#FFFF')

# The _repr_ method returns a string suitable for printing in a FASTQ file:

print('Test Sequence 1:')
print(seq1)

# Print the attributes:

print_info(seq1)

# Compress the sequence, print the attributes again:

seq1.pack()
print_info(seq1)