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minor edits to format mcsm data like sorting df

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This commit is contained in:
Tanushree Tunstall 2020-07-09 11:15:56 +01:00
parent 01fbc2a87b
commit 6402990154
4 changed files with 127 additions and 85 deletions
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6
mcsm/mcsm_wrapper.py
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@ -76,7 +76,8 @@ if DEBUG:
print('DEBUG: mCSM output CSV file:', mcsm_output)
# format_results globals
out_filename_format = gene.lower() + '_mcsm_processed.csv'
#out_filename_format = gene.lower() + '_mcsm_processed.csv'
out_filename_format = gene.lower() + '_complex_mcsm_norm.csv'
outfile_format = outdir + '/' + out_filename_format
if DEBUG:
print('DEBUG: formatted CSV output:', outfile_format)
@ -111,7 +112,6 @@ def submit_mcsm():
, 'minutes, but will be longer for more mutations.')
#%%=====================================================================
def get_results():
output_df = pd.DataFrame()
url_counter = 1 # HURR DURR COUNT STARTEDS AT ONE1`!1
success_counter = 1
@ -152,7 +152,7 @@ def format_results():
print('Finished writing file:'
, '\nFile:', outfile_format
, '\nExpected no. of rows:', len(mcsm_df_formatted)
, '\nExpected no. of cols:', len(mcsm_df_formatted)
, '\nExpected no. of cols:', len(mcsm_df_formatted.columns)
, '\n=============================================================')
#%%=====================================================================
def main():