From d011ddfa1fe7a1278c782a79c5de3263d9e70a60 Mon Sep 17 00:00:00 2001 From: Jannes Spangenberg Date: Tue, 21 Mar 2023 15:33:23 +0100 Subject: [PATCH] Fixed Nanosherlock Call - changed the way the subscript "nanosherlock" is called from magnipore - fixed path --- magnipore/magnipore.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/magnipore/magnipore.py b/magnipore/magnipore.py index 1b9c62f..e181e4b 100755 --- a/magnipore/magnipore.py +++ b/magnipore/magnipore.py @@ -25,7 +25,7 @@ LOGGER : Logger = None FONTSIZE = 18 TIMEIT = False -SUBSCRIPT = 'nanosherlock.py' +SUBSCRIPT = 'nanosherlock' def truncate_colormap(cmap, minval=0.0, maxval=1.0, n=100): new_cmap = colors.LinearSegmentedColormap.from_list( @@ -694,7 +694,7 @@ def main(): if not os.path.exists(red_first_sample) or not os.path.exists(path_to_reference_first_sample) or force_rebuild: - command_first_sample = f'python3 {os.path.join(basedir, SUBSCRIPT)} {path_to_fast5_first_sample} {path_to_reference_first_sample} {working_dir} {first_sample_label} -t {threads} -mx {mx} -mk {mk}' + command_first_sample = f'{SUBSCRIPT} {path_to_fast5_first_sample} {path_to_reference_first_sample} {working_dir} {first_sample_label} -t {threads} -mx {mx} -mk {mk}' if fast5_out: command_first_sample += ' --fast5_out' @@ -734,7 +734,7 @@ def main(): red_sec_sample = os.path.join(working_dir, 'magnipore', sec_sample_label, f'{sec_sample_label}.red') if not os.path.exists(red_sec_sample) or not os.path.exists(path_to_reference_sec_sample) or force_rebuild: - command_sec_sample = f'python3 {os.path.join(basedir, SUBSCRIPT)} {path_to_fast5_sec_sample} {path_to_reference_sec_sample} {working_dir} {sec_sample_label} -t {threads} -mx {mx} -mk {mk}' + command_sec_sample = f'{SUBSCRIPT} {path_to_fast5_sec_sample} {path_to_reference_sec_sample} {working_dir} {sec_sample_label} -t {threads} -mx {mx} -mk {mk}' if fast5_out: command_sec_sample += ' --fast5_out'