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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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57
scripts/data_extraction.py
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@ -93,13 +93,13 @@ if not datadir:
datadir = homedir + '/' + 'git/Data' datadir = homedir + '/' + 'git/Data'
if not indir: if not indir:
indir = datadir + '/' + drug + '/input_v2' indir = datadir + '/' + drug + '/input'
if not outdir: if not outdir:
outdir = datadir + '/' + drug + '/output_v2' outdir = datadir + '/' + drug + '/output'
if make_dirs: 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: try:
os.makedirs(datadir, exist_ok = True) os.makedirs(datadir, exist_ok = True)
print("Directory '%s' created successfully" %datadir) 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'].value_counts()
gene_LF3['drtype_numeric'].value_counts() gene_LF3['drtype_numeric'].value_counts()
#%% Multimode: drtype # Multimode: drtype
#============================= #=============================
# Recalculation: Revised drtype # Recalculation: Revised drtype
# max(multimode) # max(multimode)
@ -1520,7 +1520,7 @@ gene_LF3['dst_multimode'].value_counts()
# Now get the max from multimode # 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_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_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 # sanity checks
#gene_LF3['dst_noNA'].equals(gene_LF3['dst_mode']) #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=============================================================' , '\n============================================================='
, '\nPost resolving ambiguity\n' , '\nPost resolving ambiguity\n'
, ambig_muts_rev_df['mutation_info_REV'].value_counts()) , 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, print(u'\u2698' * 50,
'\nEnd of script: Data extraction and writing files' '\nEnd of script: Data extraction and writing files'