From 46b1505fdf43feaba2c22e1d05399057df300a59 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Tue, 14 Jul 2020 12:59:40 +0100 Subject: [PATCH] remove white space in colnames before mcsm format output --- mcsm/ind_scripts/format_results.py | 3 +++ mcsm/ind_scripts/format_results_notdef.py | 3 +++ mcsm/mcsm.py | 3 +++ 3 files changed, 9 insertions(+) diff --git a/mcsm/ind_scripts/format_results.py b/mcsm/ind_scripts/format_results.py index e2b05b0..e80a1c6 100755 --- a/mcsm/ind_scripts/format_results.py +++ b/mcsm/ind_scripts/format_results.py @@ -308,6 +308,9 @@ def format_mcsm_output(mcsm_outputcsv): print('Sorting df by position') mcsm_data_fs = mcsm_data_f.sort_values(by = ['position']) print('sorted df:\n', mcsm_data_fs.head()) + + # Remove white space everywhere before output: bit me when merging!? + mcsm_data_fs.columns = mcsm_data_fs.columns.str.replace(' ', '') #%%=========================================================================== ############# # sanity check before writing file diff --git a/mcsm/ind_scripts/format_results_notdef.py b/mcsm/ind_scripts/format_results_notdef.py index 7dc0450..8d442d7 100755 --- a/mcsm/ind_scripts/format_results_notdef.py +++ b/mcsm/ind_scripts/format_results_notdef.py @@ -298,6 +298,9 @@ else: , '\nis', expected_ncols_toadd, 'the no. of expected cols to add?' , '\n===============================================================') #%%============================================================================ +# Remove white space everywhere before output: bit me when merging!? +mcsm_data_fs.columns = mcsm_data_fs.columns.str.replace(' ', '') + # writing file print('Writing formatted df to csv') mcsm_data_fs.to_csv(outfile_mcsm_norm, index = False) diff --git a/mcsm/mcsm.py b/mcsm/mcsm.py index 96c2bdb..3656fd7 100644 --- a/mcsm/mcsm.py +++ b/mcsm/mcsm.py @@ -425,6 +425,9 @@ def format_mcsm_output(mcsm_outputcsv): print('Sorting df by position') mcsm_data_fs = mcsm_data_f.sort_values(by = ['position']) print('sorted df:\n', mcsm_data_fs.head()) + + # Remove white space everywhere before output: bit me when merging!? + mcsm_data_fs.columns = mcsm_data_fs.columns.str.replace(' ', '') #%%===================================================================== ############# # sanity check before writing file