got to the lineage extraction bit
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0867827ec6
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1371704685
1 changed files with 174 additions and 19 deletions
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@ -260,7 +260,6 @@ print("\n================================"
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, "\nMissing lineage samples:", meta_data['id'].nunique() - meta_data['lineage'].value_counts().sum()
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, "\n================================")
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meta_data['id'].nunique()
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meta_data['sample'].nunique()
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meta_data['id'].equals(meta_data['sample'])
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@ -1133,12 +1132,12 @@ gene_LF1.sort_values(by = ['position'], inplace = True)
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bar = gene_LF1['position'].value_counts()
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# FIXME:Can only compare identically-labeled Series objects
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if (foo == bar).all():
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print('PASS: df ordered by position')
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print(gene_LF1['position'].head())
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else:
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print('FAIL: df could not be ordered. Check source')
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sys.exit()
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#if (foo == bar).all():
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# print('PASS: df ordered by position')
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# print(gene_LF1['position'].head())
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#else:
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# print('FAIL: df could not be ordered. Check source')
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# sys.exit()
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#%% Create a copy of mutationinformation column for downstream mergeing
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gene_LF1['Mut'] = gene_LF1['mutationinformation']
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@ -1238,7 +1237,7 @@ del(out_filename_metadata_poscounts)
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#%% Add column: aa_calcprop
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#%% NEW mappings: gene_LF2
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# gene_LF2: copy gene_LF1
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gene_LF2 = gene_LF1.copy()gene_LF3.groupby('mutationinformation').drtype_all_vals.apply(list)
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gene_LF2 = gene_LF1.copy()
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gene_LF2.index
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#%% Add total unique id count
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@ -1344,7 +1343,6 @@ gene_LF3.head()
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foo = gene_LF3[['Mut', 'position', 'drtype', 'drtype_multimode', 'drtype_mode', 'drtype_max']]
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foo2 = foo.sort_values(['position', 'Mut'])
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###############################################################################
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#%% Mapping 2: column '<dst>', drug
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@ -1355,6 +1353,7 @@ foo2 = foo.sort_values(['position', 'Mut'])
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dm_om_label_map = {dr_muts_col: 'DM'
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, other_muts_col: 'OM'}
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dm_om_label_map
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gene_LF3['mutation_info_labels'] = gene_LF3['mutation_info'].map(dm_om_label_map)
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# mapping 1.2: numeric
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@ -1418,10 +1417,9 @@ gene_LF3['dst_multimode']
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gene_LF3['dst_mode'] = gene_LF3['dst_multimode'].apply(lambda x: np.nanmax(x))
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# sanity checks
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gene_LF3['dst_noNA'].equals(gene_LF3['dst_mode'])
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#gene_LF3['dst_noNA'].equals(gene_LF3['dst_mode'])
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gene_LF3[drug].value_counts()
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gene_LF3['dst_noNA'].value_counts()
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#gene_LF3['dst_noNA'].value_counts()
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gene_LF3['dst_mode'].value_counts()
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foo = gene_LF3[['Mut', 'position', 'dst', 'dst_multimode', 'dst_noNA', 'dst_mode']]
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@ -1443,10 +1441,10 @@ print('\n------------------------------------------------------'
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, gene_LF3['dst_mode'].value_counts()
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, '\nTotal samples [revised]', gene_LF3['dst_mode'].value_counts().sum()
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, '\n----------------------------------'
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, '\nRevised drug column count: dst_noNA\n'
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, '\n----------------------------------\n'
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, gene_LF3['dst_noNA'].value_counts()
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# , '\n----------------------------------'
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# , '\nRevised drug column count: dst_noNA\n'
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# , '\n----------------------------------\n'
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# , gene_LF3['dst_noNA'].value_counts()
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)
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#%% Create revised mutation_info_column based on dst_mode
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#---------------------------------------
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@ -1462,8 +1460,8 @@ gene_LF3['mutation_info_labels_v1'].value_counts() == gene_LF3['mutation_info_la
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# Now overwrite
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gene_LF3['mutation_info_labels_dst'] = gene_LF3['dst_mode'].map({1: 'DM', 0: 'OM'})
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gene_LF3['mutation_info_labels'] = gene_LF3['dst_mode'].map({1: 'DM', 0: 'OM'})
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if (gene_LF3['mutation_info_labels_dst'].value_counts() == gene_LF3['mutation_info_labels'].value_counts()):
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print('\nRevised mutation_info colum created')
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if all(gene_LF3['mutation_info_labels_dst'].value_counts() == gene_LF3['mutation_info_labels'].value_counts()):
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print('\nPASS: Revised mutation_info column created successfully')
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gene_LF3 = gene_LF3.drop(['mutation_info_labels_dst'], axis = 1)
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else:
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print('\nmutation info labels numbers mismatch'
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@ -1474,6 +1472,11 @@ gene_LF3['mutation_info_orig'].value_counts()
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gene_LF3['mutation_info_labels_orig'] = gene_LF3['mutation_info_orig'].map(dm_om_label_map)
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gene_LF3['mutation_info_labels_orig'].value_counts()
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#%% FIXME: Get multimode for dm_om_numeric column
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#dm_om_multimode_LF4 = gene_LF3.groupby('mutationinformation')['dm_om_numeric_orig'].agg(multimode)
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#dm_om_multimode_LF4
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#gene_LF3['dst_multimode_numeric'] = gene_LF3['dst_multimode'].fillna(dm_om_multimode_LF4)
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# %% sanity check for the revised dst
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gene_LF3[drug].value_counts()
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gene_LF3[drug].value_counts().sum()
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@ -1485,4 +1488,156 @@ gene_LF3['dst_mode'].value_counts().sum()
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# direct comparision
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gene_LF3['dst'].value_counts()
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gene_LF3['mutation_info_labels'].value_counts()
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#%%
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#%% Lineage
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gene_LF3['lineage'].value_counts()
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# lineage_label_numeric = {'lineage1' : 1
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# , 'lineage2' : 2
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# , 'lineage3' : 3
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# , 'lineage4' : 4
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# , 'lineage5' : 5
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# , 'lineage6' : 6
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# , 'lineage7' : 7
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# , 'lineageBOV' : 8}
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lineage_label_numeric = {'L1' : 1
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, 'L2' : 2
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, 'L3' : 3
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, 'L4' : 4
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, 'L5' : 5
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, 'L6' : 6
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, 'L7' : 7
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, 'LBOV' : 8}
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lineage_label_numeric
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# copy column to allow cross checks after stripping white space
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gene_LF3['lineage'] = gene_LF3['lineage'].str.strip()
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gene_LF3['lineage_corrupt'] = gene_LF3['lineage']
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#all(gene_LF3['lineage_corrupt'].value_counts() ==gene_LF3['lineage'].value_counts())
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gene_LF3['lineage_corrupt'].value_counts()
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#%%tidy_split(): Lineage
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# Create df with tidy_split: lineage
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lf_lin_split = tidy_split(gene_LF3, 'lineage_corrupt', sep = ';')
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lf_lin_split['lineage_corrupt'] = lf_lin_split['lineage_corrupt'].str.strip()
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lf_lin_split['lineage_corrupt'].value_counts()
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# Map lineage labels to numbers to allow metrics
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lf_lin_split['lineage_numeric'] = lf_lin_split['lineage_corrupt'].map(lineage_label_numeric)
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lf_lin_split['lineage_numeric'].value_counts()
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#--------------------------------
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# Lineage_corrupt ALL values:
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#--------------------------------
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# Add all lineages for each mutation
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lf_lin_split['lineage_corrupt_list'] = lf_lin_split['lineage_corrupt']
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lf_lin_split['lineage_corrupt_list'].value_counts()
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#lf_lin_split['lineage_corrupt_list'] = lf_lin_split['mutationinformation'].map(lf_lin_split.groupby('mutationinformati
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lf_lin_split['lineage_corrupt_list'] = lf_lin_split.groupby('mutationinformation').lineage_corrupt_list.apply(list)
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lf_lin_split['lineage_corrupt_list'].value_counts()
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# Add lineage unique count
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lf_lin_split['lineage_corrupt_ucount'] = lf_lin_split['Mut'].map(lf_lin_split.groupby('Mut')['lineage_corrupt'].nunique())
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#lf_lin_split['lineage_corrupt_ucount'] = lf_lin_split['lineage_corrupt']
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lf_lin_split['lineage_corrupt_ucount'].value_counts()
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# Add lineage_set
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lf_lin_split['lineage_set'] = lf_lin_split['lineage_corrupt_list'].apply(lambda x : set(list(x)))
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lf_lin_split['lineage_ulist'] = lf_lin_split['lineage_set'].apply(lambda x : list(x))
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#-------------------------------------
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# Lineage numeric mode: multimode
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#-------------------------------------
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lf_lin_split['lineage_multimode'] = lf_lin_split.groupby('mutationinformation')['lineage_numeric'].agg(multimode)
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lf_lin_split['lineage_multimode'].value_counts()
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# cant take max as it doesn't mean anyting!
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foo = lf_lin_split[['Mut', 'lineage_ulist']]
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###############################################################################
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#%% Final merge: gene_LF4 with lineage_split_df
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gene_LF4 = gene_LF3.copy()
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gene_LF4.index
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gene_LF4['index_orig_copy'] = gene_LF4['index_orig']
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lf_lin_split['index_orig_copy'] = lf_lin_split['index_orig']
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#================================
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# Merge with gene_LF3 with
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# lf_lin_split baseed on index
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#================================
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# set index for lf_lin_split
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lf_lin_split.index
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lf_lin_split.reset_index(inplace=True)
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lf_lin_split['mutationinformation']
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lf_lin_split = lf_lin_split.set_index(['index_orig_copy'])
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lf_lin_split.index
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# set index for gene_LF4
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gene_LF4.index
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gene_LF4.reset_index(inplace=True)
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gene_LF4.index
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gene_LF4['mutationinformation']
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gene_LF4['index_orig_copy']
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gene_LF4 = gene_LF4.set_index(['index_orig_copy'])
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gene_LF4.index
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#-------------------------
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# colum lineage_ucount:
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# contribution of each distinct lineage
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#-------------------------
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gene_LF4['lineage_ucount'] = gene_LF4['lineage']
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#-------------------------
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# colum lineage list:
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#-------------------------
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#gene_LF4['lineage_set'] = gene_LF4['lineage']
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gene_LF4['lineage_ulist'] = gene_LF4['lineage']
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gene_LF4['lineage_list'] = gene_LF4['lineage']
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#-------------------------
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# colum lineage_list mode:
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#-------------------------
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gene_LF4['lineage_mode'] = gene_LF4['lineage']
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# merge based on indices
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gene_LF4.index.nunique()
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lf_lin_split.index.nunique()
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all(gene_LF4.index.isin(lf_lin_split.index))
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all(lf_lin_split.index.isin(gene_LF4.index))
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gene_LF4.index
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lf_lin_split.index
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if (gene_LF4.index.nunique() == lf_lin_split.index.nunique()) and ( all(gene_LF4.index.isin(lf_lin_split.index)) == all(lf_lin_split.index.isin(gene_LF4.index)) ):
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print('\nPass: merging lineage_ucount with gene_LF4')
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else:
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sys.exit('\nFail: Indices mismatch, cannot merge! Quitting!')
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###########################
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# magic merge happens here
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###########################
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lf_lin_split.index.drop_duplicates(keep='first')
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lf_lin_split = lf_lin_split
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lf_lin_split_U = lf_lin_split[~lf_lin_split.index.duplicated(keep='first')]
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lf_lin_split_U.shape
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gene_LF4.loc[lf_lin_split_U.index, 'lineage_ucount'] = lf_lin_split_U['lineage_corrupt_ucount']
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gene_LF4['lineage_ucount'].value_counts()
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#gene_LF4.loc[lf_lin_split_U.index, 'lineage_set'] = lf_lin_split_U['lineage_set']
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#gene_LF4['lineage_set'].value_counts()
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gene_LF4.loc[lf_lin_split_U.index, 'lineage_ulist'] = lf_lin_split_U['lineage_ulist']
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gene_LF4['lineage_ulist'].value_counts()
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gene_LF4.loc[lf_lin_split_U.index, 'lineage_list'] = lf_lin_split_U['lineage_corrupt_list']
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gene_LF4['lineage_list'].value_counts()
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gene_LF4.loc[lf_lin_split_U.index, 'lineage_mode'] = lf_lin_split_U['lineage_multimode']
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gene_LF4['lineage_mode'].value_counts()
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foo = gene_LF4[['mutationinformation', 'lineage', 'lineage_ucount'
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#, 'lineage_set'
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, 'lineage_ulist'
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, 'lineage_mode'
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, 'lineage_list']]
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#%%
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#Subset relevant columns for output and put the rest of the output here
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