Merge pull request #113 from awitney/master

add group switch to stats option
arq5x · Jan 26, 2017 · df04069 · df04069
2 parents beb22ad + f235250
commit df04069
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Showing 2 changed files with 6 additions and 1 deletion.
diff --git 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
@@ -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()