From 221edbd262a920bf49535667d3f6d05d8beb3a2b Mon Sep 17 00:00:00 2001 From: Rachel Colquhoun Date: Tue, 3 Mar 2020 20:54:22 +0000 Subject: [PATCH] make porechop mode the default, and change command line args from single to require_two_barcodes in line with this --- readucks/readucks.py | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/readucks/readucks.py b/readucks/readucks.py index 05ddb42..26d8221 100755 --- a/readucks/readucks.py +++ b/readucks/readucks.py @@ -49,7 +49,7 @@ def main(): settings = { 'barcode_set': barcode_set, - 'single_barcode': args.single, + 'single_barcode': not args.require_two_barcodes, 'threshold': args.threshold / 100.0, 'secondary_threshold': None, 'score_diff': None, @@ -442,15 +442,15 @@ def get_arguments(): help='Writes extended information about barcode calls. ') main_group.add_argument('-s', '--summary_info', action='store_true', help='Writes another file with information about barcode calls. ') - main_group.add_argument('-m', '--mode', default='stringent', - help='Demuxing mode, maximizing either ["stringent","lenient", "porechop"].') + main_group.add_argument('-m', '--mode', default='porechop', + help='Demuxing mode, one of ["stringent","lenient", "porechop"].') main_group.add_argument('-p', '--prefix', help='Optional prefix to file names') main_group.add_argument('-t', '--threads', type=int, default=2, help='The number of threads to use (1 to turn off multithreading)') main_group.add_argument('-n', '--num_reads_in_batch', type=int, default=200, help='The number of reads to process (and hold in memory) at a time') - main_group.add_argument('--check_reads', type=int, required=False, + main_group.add_argument('--check_reads', type=int, default=1000, help='Number of barcodes to classify before filtering barcode set') main_group.add_argument('--adapter_threshold', type=int, default=90, help='Identity required for a barcode to be included after filtering') @@ -458,8 +458,8 @@ def get_arguments(): help='Level of output information: 0 = none, 1 = some, 2 = lots') barcode_group = parser.add_argument_group('Demuxing options') - barcode_group.add_argument('--single', action='store_true', - help='Only attempts to match a single barcode at one end (default double)') + barcode_group.add_argument('--require_two_barcodes', action='store_true', + help='Match barcodes at both ends of read (default single)') barcode_group.add_argument('--native_barcodes', action='store_true', help='Only attempts to match the 24 native barcodes (default)') barcode_group.add_argument('--pcr_barcodes', action='store_true', @@ -473,9 +473,9 @@ def get_arguments(): barcode_search_group = parser.add_argument_group('Barcode search settings', 'Settings for how to search for and call barcodes') - barcode_search_group.add_argument('--threshold', type=float, default=90.0, + barcode_search_group.add_argument('--threshold', type=float, default=75, help='A read must have at least this percent identity to a barcode') - barcode_search_group.add_argument('--secondary_threshold', type=float, default=70.0, + barcode_search_group.add_argument('--secondary_threshold', type=float, default=65, help='The second barcode must have at least this percent identity (and match the first one)') barcode_search_group.add_argument('--score_diff', type=int, default=5, help='The second barcode must have at least this percent identity (and match the first one)') @@ -496,11 +496,11 @@ def get_arguments(): 'Error: only one of the following options may be used: --native_barcodes, --pcr_barcodes or --rapid_barcodes') if args.rapid_barcodes: - args.single = True + args.require_two_barcodes = False if args.verbosity > 0: print('Using single barcode demultiplexing for rapid barcode kit') - if (args.single and args.secondary_threshold): + if (not args.require_two_barcodes and args.secondary_threshold): args.secondary_threshold = None if args.verbosity > 0: print('Secondary threshold ignored in single barcode demultiplexing mode')