From f235250614a6ef2cc9e5b6ac118fe0efc87d4d62 Mon Sep 17 00:00:00 2001 From: Adam Witney Date: Tue, 24 Jan 2017 15:29:28 +0000 Subject: [PATCH] add group switch to stats option --- poretools/poretools_main.py | 5 +++++ poretools/stats.py | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/poretools/poretools_main.py b/poretools/poretools_main.py index 22d0aa9..a4108e5 100755 --- a/poretools/poretools_main.py +++ b/poretools/poretools_main.py @@ -212,6 +212,11 @@ def main(): default=False, action='store_true', help=('Verbose output in tab-separated format.')) + parser_stats.add_argument('--group', + dest='group', + default=0, + type=int, + help=('Base calling group serial number to extract, default 000')) parser_stats.set_defaults(func=run_subtool) diff --git a/poretools/stats.py b/poretools/stats.py index b2b9920..d22082a 100644 --- a/poretools/stats.py +++ b/poretools/stats.py @@ -43,7 +43,7 @@ def run(parser, args): logger.warning("No valid sequences observed.\n") else: sizes = [] - for fast5 in Fast5File.Fast5FileSet(args.files): + for fast5 in Fast5File.Fast5FileSet(args.files, group=args.group): fas = fast5.get_fastas(args.type) sizes.extend([len(fa.seq) for fa in fas if fa is not None]) fast5.close()