# Output parameters
parser.add_argument('-d', dest='database_filepath', required=True,
help='Path and filename of database to writ reads to.')
parser.add_argument('-f', dest='force_overwrite', action='store_true', default=False,
help='Overwrite previous tables with the same name.')
args = parser.parse_args()
toc = time.time()
if args.input == '-':
args.input = sys.stdin
# Connect/make database
db = Reads_db(db_file=args.database_filepath, recbyname=True)
if ('seqs' not in db.tables) or (args.force_overwrite == True):
db.create_seqs_table(overwrite=args.force_overwrite, read_header=args.header_format)
if ('samples' not in db.tables) or (args.force_overwrite == True):
db.create_samples_table(overwrite=args.force_overwrite)
db.load_seqs(data_files=args.input, barcode_files=args.barcodes, buffer_max=args.buffer_max,
read_header=args.header_format)
total_t = time.time() - toc
print >> sys.stderr, 'Loaded processed reads file in {0}'.format(
time.strftime('%H:%M:%S', time.gmtime(total_t)))
if __name__ == '__main__':
parser.add_argument(
"--max", dest="fmax", default=0, type=int, help="Maximum size of clusters to load. Default = 0 no max limit"
)
parser.add_argument(
"--skipsort",
dest="skipsort",
action="store_true",
help="Skip sorting the cluster file. Useful if file has already been previously sorted.",
)
args = parser.parse_args()
if os.path.exists(args.output):
db = Reads_db(args.output)
else:
raise Exception("Database file not found.")
# Load cluster file
db.load_cluster_file(
cluster_file_handle=args.input,
table_prefix=args.tableprefix,
overwrite=args.overwrite,
fmin=args.fmin,
fmax=args.fmax,
skipsort=args.skipsort,
buffer_max=args.buffer,
)
total_t = time.time() - toc
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)
Basic query is:
SELECT * FROM {clusters}
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')
