from srastream import SraReader, sra_dump

# Grab 1000 read pairs from an SRA run and write them to FASTQ files.
result = sra_dump('SRR3618567', item_limit=1000)
print("Wrote {read_count} reads from {accn} to {file1}, {file2}".format(
    **result))

# Stream all reads from an accession to a pair of FIFOs. These can be used as
# inputs to your favorite aligner to avoid the need for writing intermediate
# files.
result = sra_dump('ERR1912997', fifos=True, batch_size=1000)
print("Streamed {read_count} reads from {accn} to {file1}, {file2}".format(
    **result))

# Use the API to stream reads within your own python program.
with SraReader(accn) as reader:
    for frags in reader:
        # 'frags' is a tuple of fragments, where each fragment is
        # (name, sequence, qualities). For paired-end reads, 'frags'
        # usually (always?) has two items (read1, read2).
        print("\n".join(str(read) for read in reads))