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saving data extraction updated script

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This commit is contained in:
Tanushree Tunstall 2022-04-28 13:02:30 +01:00
parent e419d320ac
commit 5429b8fed7
1 changed files with 54 additions and 7 deletions
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59
scripts/data_extraction.py
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@ -68,7 +68,7 @@ os.getcwd()
arg_parser = argparse.ArgumentParser()
arg_parser.add_argument('-d', '--drug', help='drug name (case sensitive)', default = None)
arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = None)
arg_parser.add_argument('--datadir', help = 'Data Directory. By default, it assmumes homedir + git/Data')
arg_parser.add_argument('--datadir' , help = 'Data Directory. By default, it assmumes homedir + git/Data')
arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
arg_parser.add_argument('-m', '--make_dirs', help = 'Make dir for Data, input and output', action='store_true')
@ -93,13 +93,13 @@ if not datadir:
datadir = homedir + '/' + 'git/Data'
if not indir:
indir = datadir + '/' + drug + '/input_v2'
indir = datadir + '/' + drug + '/input'
if not outdir:
outdir = datadir + '/' + drug + '/output_v2'
outdir = datadir + '/' + drug + '/output'
if make_dirs:
print('make_dirs is turned on, creating data dir:', datadir)
print('make_dirs is turned on, creating data dir (unless it already exists):', datadir)
try:
os.makedirs(datadir, exist_ok = True)
print("Directory '%s' created successfully" %datadir)
@ -1411,7 +1411,7 @@ gene_LF3['drtype_numeric'] = gene_LF3['drtype'].map(drtype_map)
gene_LF3['drtype'].value_counts()
gene_LF3['drtype_numeric'].value_counts()
#%% Multimode: drtype
# Multimode: drtype
#=============================
# Recalculation: Revised drtype
# max(multimode)
@ -1520,7 +1520,7 @@ gene_LF3['dst_multimode'].value_counts()
# Now get the max from multimode
#gene_LF3['dst_mode'] = gene_LF3.groupby('mutationinformation')['dst_noNA'].max() # this somehow is not right!
#gene_LF3['dst_noNA'] = gene_LF3['dst_multimode'].apply(lambda x: np.nanmax(x))
gene_LF3['dst_mode'] = gene_LF3['dst_multimode'].apply(lambda x: np.nanmax(x))
gene_LF3['dst_mode'] = gene_LF3['dst_multimode'].apply(lambda x: np.nanmax(x)) #ML
# sanity checks
#gene_LF3['dst_noNA'].equals(gene_LF3['dst_mode'])
@ -1969,6 +1969,53 @@ if dr_muts.isin(other_muts).sum() & other_muts.isin(dr_muts).sum() > 0:
, '\n============================================================='
, '\nPost resolving ambiguity\n'
, ambig_muts_rev_df['mutation_info_REV'].value_counts())
print('\n============================================================='
, '\n============================================================='
, '\###############################\n'
, '\nNumbers for ML workflows...'
, '\n###############################\n'
, '\ncolumn name [drug, old]:', drug, '\n'
, gene_LF4[drug].value_counts()
, '\nTotal drug samples[old]:', gene_LF4[drug].value_counts().sum()
, '\nPercentages:\n'
, gene_LF4[drug].value_counts(normalize = True)
, '\n-------------------------------------------------------------'
, '\ncolumn name [drug, revised]: dst_mode\n'
, gene_LF4['dst_mode'].value_counts()
, '\nTotal drug samples[revised]:', gene_LF4['dst_mode'].value_counts().sum()
, '\nPercentages:\n'
, gene_LF4['dst_mode'].value_counts(normalize = True)
, '\n-------------------------------------------------------------'
, '\n-------------------------------------------------------------'
, '\ncolumn name: drtye_mode\n'
, gene_LF4['drtype_mode'].value_counts()
, '\nTotal drtype_mode:', gene_LF4['drtype_mode'].value_counts().sum()
, '\nPercentages:\n'
, gene_LF4['drtype_mode'].value_counts(normalize = True)
, '\n-------------------------------------------------------------'
, '\n-------------------------------------------------------------'
, '\ncolumn name [dm_om, old]: mutation_info_orig\n'
, gene_LF4['mutation_info_orig'].value_counts()
, '\nTotal mutation_info_orig:', gene_LF4['mutation_info_orig'].value_counts().sum()
, '\nPercentages:\n'
, gene_LF4['mutation_info_orig'].value_counts(normalize = True)
, '\n-------------------------------------------------------------'
, '\n-------------------------------------------------------------'
, '\ncolumn name [dm_om, revised]: mutation_info\n'
, gene_LF4['mutation_info'].value_counts()
, '\nTotal mutation_info:', gene_LF4['mutation_info'].value_counts().sum()
, '\nPercentages:\n'
, gene_LF4['mutation_info'].value_counts(normalize = True)
, '\n-------------------------------------------------------------'
, '\n============================================================='
)
#=======================================================================
print(u'\u2698' * 50,
'\nEnd of script: Data extraction and writing files'