help='number of reads to use for AGS estimation (default = 1e6)')
parser.add_argument('-l', dest='read_length', type=int,
help='trim reads to this length (default = median read length)',
choices=[50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 175, 200, 225, 250, 300, 350, 400, 450, 500])
parser.add_argument('-f', dest='file_type', type=str,
help='file type (default = autodetect)',
choices=['fasta', 'fastq'])
parser.add_argument('-c', dest='fastq_format', type=str,
help='quality score encoding (default = autodetect)',
choices=['fastq-sanger', 'fastq-solexa', 'fastq-illumina'])
parser.add_argument('-t', dest='threads', type=int, default=1,
help='number of threads to use for database search (default = 1)')
parser.add_argument('-q', dest='min_quality', type=int, default=-5,
help='minimum base-level PHRED quality score (default = -5; no filtering)')
parser.add_argument('-m', dest='mean_quality', type=int, default=-5,
help='minimum read-level PHRED quality score (default = -5; no filtering)')
parser.add_argument('-d', dest='filter_dups', action='store_true', default=False,
help='filter duplicate reads (default = False)')
parser.add_argument('-u', dest='max_unknown', type=int, default=100,
help='max percent of unknown bases (default = 100 percent; no filtering)')
parser.add_argument('-k', dest='keep_tmp', action='store_true', default=False,
help='keep temporary files (default = False)')
parser.add_argument('-s', dest='quiet', action='store_true', default=False,
help='suppress printing program\'s progress to stdout (default = False)')
args = vars(parser.parse_args())
# run pipeline
est_ags, args = microbe_census.run_pipeline(args)
# write output
microbe_census.report_results(args, est_ags)
def setUp(self):
self.expected = 3530599.61
self.infile = os.path.join(data_dir, 'metagenome.fa.gz')
self.observed = microbe_census.run_pipeline({'seqfiles':[self.infile]})[0]
help="file type (default = autodetect)",
choices=["fasta", "fastq"])
type.add_argument('-c', dest='fastq_format', type=str,
help="quality score encoding (default = autodetect)",
choices=["fastq-sanger", "fastq-solexa", "fastq-illumina"])
qc = parser.add_argument_group('Quality control (optional)')
qc.add_argument('-l', dest='read_length', type=int,
help="all reads trimmed to this length; reads shorter than this discarded (default = median read length)",
choices=[50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 175, 200, 225, 250, 300, 350, 400, 450, 500])
qc.add_argument('-q', dest='min_quality', type=int, default=-5,
help="minimum base-level PHRED quality score (default = -5; no filtering)")
qc.add_argument('-m', dest='mean_quality', type=int, default=-5,
help="minimum read-level PHRED quality score (default = -5; no filtering)")
qc.add_argument('-d', dest='filter_dups', action='store_true', default=False,
help="filter duplicate reads (default = False)")
qc.add_argument('-u', dest='max_unknown', type=int, default=100,
help="max percent of unknown bases per read (default = 100 percent; no filtering)")
args = vars(parser.parse_args())
args['seqfiles'] = args['seqfiles'].split(',')
# run pipeline
from microbe_census import microbe_census
est_ags, args = microbe_census.run_pipeline(args)
if not args['no_equivs']: count_bases = microbe_census.count_bases(args)
else: count_bases = None
# write output
microbe_census.report_results(args, est_ags, count_bases)
