help='''SQL expression to filter the query which selects the sequences in the database. Default is to export all sequences in database.
Basic query is:
SELECT seqid, seq, phred FROM seqs INNER JOIN samples ON seqs.sampleId=samples.sampleId
WHERE <filter_expression> ''')
parser.add_argument('-s', dest='startidx',
default=0,
help='Starting base index of DNA sequences that are written to file, used to miss out cutsite if desired.')
parser.add_argument('-f', dest='format',
default='fasta',
help='Format of file written to output.')
parser.add_argument('-b', dest='rowbuffer',
default=100000,
help='Read write buffer. Number of records to read before writing to file.')
parser.add_argument('-F', dest='overwrite',
default=False,
help='Overwrite any file with same name as output.')
args = parser.parse_args()
# Write records to output
db = Reads_db(args.input, recbyname=True)
fastafile_handle = db.write_reads(args.output, output_format=args.format,
filter_expression=args.filter_expression,
startidx=args.startidx,
rowbuffer=args.rowbuffer,
overwrite=args.overwrite)
WHERE <filter_expression> ''')
parser.add_argument('-s', dest='startidx',
default=0,
help='Starting base index of DNA sequences that are written to file, used to miss out cutsite if desired.')
parser.add_argument('-f', dest='format',
default='fasta',
help='Format of file written to output.')
print sys.argv
args = parser.parse_args()
# Write records to output
db = Reads_db(args.input, recbyname=True)
clusters_list = db.get_cluster_by_size()
fastafile_handle = db.write_reads(args.output, format=args.format,
filter_expression=args.filter_expression,
startidx=args.startidx)
if args.query_expression:
fastafile_handle = db.write_reads(args.pattern, args.output,
use_type_column=args.typeflag, format='fasta')
