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Merge branch 'gidb_dev' (including merge conflict while after adding CLI arguments for mcsm_na/format_results_mcsm_na.py)

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Tanushree Tunstall 2021-10-28 12:45:39 +01:00
commit e2bc1cdde1
70 changed files with 4048 additions and 819 deletions
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9
mcsm_na/format_results_mcsm_na.py
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@ -51,7 +51,7 @@ def format_mcsm_na_output(mcsm_na_output_tsv):
print('Assigning meaningful colnames'
, '\n=======================================================')
my_colnames_dict = {'PDB_FILE': 'pdb_file' # relevant info from this col will be extracted and the column discarded
, 'CHAIN': 'chain' # {wild_type}<position>{mutant_type}
, 'CHAIN': 'chain'
, 'WILD_RES': 'wild_type' # one letter amino acid code
, 'RES_POS': 'position' # number
, 'MUT_RES': 'mutant_type' # one letter amino acid code
@ -65,8 +65,8 @@ def format_mcsm_na_output(mcsm_na_output_tsv):
#############
# create mutationinformation column
#############
mcsm_na_data['mutationinformation'] = mcsm_na_data['wild_type'] + mcsm_na_data.position.map(str) + mcsm_na_data['mutant_type']
#mcsm_na_data['mutationinformation'] = mcsm_na_data['wild_type'] + mcsm_na_data.position.map(str) + mcsm_na_data['mutant_type']
mcsm_na_data['mutationinformation'] = mcsm_na_data.loc[:,'wild_type'] + mcsm_na_data.loc[:,'position'].astype(int).apply(str) + mcsm_na_data.loc[:,'mutant_type']
#%%=====================================================================
#############
# Create col: mcsm_na_outcome
@ -131,5 +131,4 @@ def format_mcsm_na_output(mcsm_na_output_tsv):
, 'chain'
, 'pdb_file']]
return(mcsm_na_dataf)
#%%#####################################################################
#%%#####################################################################