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test_data/processing_custom.py
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test_data/processing_custom.py
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Thu Mar 24 15:01:59 2022
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@author: tanu
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"""
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import sys, os
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import pandas as pd
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import numpy as np
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from statistics import mean, median, mode
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from statistics import multimode
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from collections import Counter
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from tidy_split import tidy_split
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#import math
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# https://stackoverflow.com/questions/43321455/pandas-count-null-values-in-a-groupby-function
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# https://stackoverflow.com/questions/33457191/python-pandas-gene_LF2frame-fill-nans-with-a-conditional-mean
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# round up
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# int(math.ceil(mean(foo)))
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# https://stackoverflow.com/questions/33457191/python-pandas-gene_LF2frame-fill-nans-with-a-conditional-mean
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# https://stackoverflow.com/questions/37189878/pandas-add-column-to-groupby-gene_LF2frame
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# https://stackoverflow.com/questions/43847520/how-to-get-the-distinct-count-of-values-in-a-python-pandas-gene_LF2frame
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#%% Read gene_LF2 and formatting
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drug = "pyrazinamide"
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gene_LF2 = pd.read_csv("/home/tanu/git/ML_AI_training/test_gene_LF2/sample_gene_LF2.csv")
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gene_LF2.columns
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gene_LF2.head()
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#%% Quick checks: Lineage and sample count for each mutation
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gene_LF2['id'].nunique()
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gene_LF2['mutationinformation'].nunique()
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total_id_ucount = gene_LF2['id'].nunique()
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total_id_ucount
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gene_LF2.groupby('mutationinformation')['lineage'].size()
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gene_LF2.groupby('mutationinformation')['lineage_corrupt'].size()
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gene_LF2.groupby('mutationinformation')['id'].size()
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gene_LF2.groupby('mutationinformation')['lineage'].value_counts()
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gene_LF2.groupby('mutationinformation')['lineage'].nunique()
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#%% id count: add all id ids and count of unique ids per mutation
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gene_LF2['id_list'] = gene_LF2['mutationinformation'].map(gene_LF2.groupby('mutationinformation')['id'].apply(list))
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gene_LF2['id_ucount'] = gene_LF2['mutationinformation'].map(gene_LF2.groupby('mutationinformation')['id'].nunique())
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gene_LF2[['mutationinformation', 'id', 'id_list', 'id_ucount']]
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#%% Lineages: add all lineages and count of unique lineages per mutation
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# Lineages good: lineage column has only a single lineage for each mutationinformation
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gene_LF2['lineage']
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gene_LF2['lineage_list'] = gene_LF2['mutationinformation'].map(gene_LF2.groupby('mutationinformation')['lineage'].apply(list))
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gene_LF2['lineage_ucount'] = gene_LF2['mutationinformation'].map(gene_LF2.groupby('mutationinformation')['lineage'].nunique())
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gene_LF2[['mutationinformation', 'lineage', 'lineage_list', 'lineage_ucount']]
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# Lineage corrupt: lineage column has only multiple lineages for each mutationinformation separated by ';'
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gene_LF2['lineage_corrupt']
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# split using tidy_split()
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gene_LF2_split = tidy_split(gene_LF2, 'lineage_corrupt', sep = ';')
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# remove leading white space else these are counted as distinct mutations as well
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#gene_LF2_split['lineage_corrupt'] = gene_LF2_split['lineage_corrupt'].str.lstrip()
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gene_LF2_split['lineage_corrupt'] = gene_LF2_split['lineage_corrupt'].str.strip()
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gene_LF2_split.head()
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gene_LF2_split['lineage_corrupt_list'] = gene_LF2_split['mutationinformation'].map(gene_LF2_split.groupby('mutationinformation')['lineage_corrupt'].apply(list))
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gene_LF2_split['lineage_corrupt_ucount'] = gene_LF2_split['mutationinformation'].map(gene_LF2_split.groupby('mutationinformation')['lineage_corrupt'].nunique())
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gene_LF2_split[['mutationinformation', 'lineage_corrupt_list', 'lineage_corrupt_ucount']]
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gene_LF2_split[['mutationinformation', 'lineage_ucount', 'lineage_corrupt_ucount']]
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#%% AF: calculate AF for each mutation
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#1) calculate no. of unique ids
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gene_LF2['id_ucount']/total_id_ucount
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#%% DM OM labels
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# COPY mutation_info_labels column
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gene_LF2['mutation_info_labels_orig'] = gene_LF2['mutation_info_labels']
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# Convert DM/OM labels to numeric
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dm_om_map = {'DM': 1, 'OM': 0} # pnca, OM is minority, other genes: DM is minority
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gene_LF2['dm_om_numeric'] = gene_LF2['mutation_info_labels'].map(dm_om_map)
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# sanity check
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gene_LF2['dm_om_numeric'].value_counts()
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gene_LF2['mutation_info_labels'].value_counts()
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# Convert drtype column to numeric
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drtype_map = {'XDR': 5
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, 'Pre-XDR': 4
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, 'MDR': 3
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, 'Pre-MDR': 2
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, 'Other': 1
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, 'Sensitive': 0}
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gene_LF2['drtype_numeric'] = gene_LF2['drtype'].map(drtype_map)
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# COPY dst column
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gene_LF2['dst'] = gene_LF2[drug] # to allow cross checking
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gene_LF2['dst_multimode'] = gene_LF2[drug]
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# sanity check
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gene_LF2[drug].value_counts()
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gene_LF2['dst_multimode'].value_counts()
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gene_LF2[drug].isnull().sum()
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gene_LF2['dst_multimode'].isnull().sum()
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gene_LF2['mutationinformation'].value_counts()
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#gene_LF2.C.isnull().groupby([df['A'],df['B']]).sum().astype(int).reset_index(name='count')
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gene_LF2[drug].isnull().groupby(gene_LF2['mutationinformation']).sum()
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# GOAL is to populate na in the dst column from the count of the dm_om_numeric column
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gene_LF2['dst_multimode'].isnull().groupby(gene_LF2['mutationinformation']).sum()
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gene_LF2['mutationinformation']
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#%% Recalculating dst: my gene_LF2
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#------------------------------
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# Revised dst: max(multimode)
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#------------------------------
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# For each mutation, generate the revised dst which is the mode of dm_om_numeric
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# PROBLEM: Returns the smallest of the two when bimodal, and fails when all equally likely
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# SOLUTION: Using max of the 'dst_noNA' column
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#gene_LF22.groupby('mutationinformation')['dm_om_numeric'].agg(multimode)
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# Get multimode for dm_om_numeric column
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dm_om_multimode = gene_LF2.groupby('mutationinformation')['dm_om_numeric'].agg(multimode)
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#dm_om_multimode
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# Fill using multimode ONLY where NA in dst_multimode column
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#gene_LF22['dst_multimode'] = gene_LF22['dst_multimode'].fillna(dm_om_multimode)
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gene_LF2['dst_multimode'] = gene_LF2['dst_multimode'].fillna(dm_om_multimode)
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# gene_LF22['dst_multimode']
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# Now get the max from multimode
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gene_LF22['dst_noNA'] = gene_LF2['dst_multimode'].apply(lambda x: np.nanmax(x))
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print(gene_LF2)
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# Finally created a revised dst with the max from the multimode
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gene_LF22['dst_mode'] = gene_LF2.groupby('mutationinformation')['dst_noNA'].max()
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#==============================================================================
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#%% Recalculating drtype: my gene_LF2
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#--------------------------------
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# drtype: ALL values:
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# numeric and names in an array
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#--------------------------------
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gene_LF2['drtype_all_vals'] = gene_LF2['drtype_numeric']
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gene_LF2['drtype_all_names'] = gene_LF2['drtype']
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# example: https://stackoverflow.com/questions/55125680/pandas-get-all-groupby-values-in-an-array
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# print(df.groupby('key').gene_LF2.apply(list).reset_index()) # my use case, don't need the reset_index()
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gene_LF2['drtype_all_vals'] = gene_LF2.groupby('mutationinformation').drtype_all_vals.apply(list)
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gene_LF2['drtype_all_names'] = gene_LF2.groupby('mutationinformation').drtype_all_names.apply(list)
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#---------------------------------
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# Revised drtype: max(Multimode)
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#--------------------------------
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gene_LF2['drtype_multimode'] = gene_LF2.groupby(['mutationinformation'])['drtype_numeric'].agg(multimode)
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gene_LF2['drtype_multimode']
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# Now get the max from multimode
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gene_LF2['drtype_mode'] = gene_LF2['drtype_multimode'].apply(lambda x: np.nanmax(x))
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gene_LF2.head()
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#----------------------
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# Revised drtype: Max
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#----------------------
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gene_LF2.head()
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gene_LF2['drtype_max'] = gene_LF2.groupby(['mutationinformation'])['drtype_numeric'].max()
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#gene_LF2 = gene_LF22.reset_index()
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gene_LF2.head()
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#%% Finally reset index
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gene_LF2 = gene_LF2.reset_index()
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#==============================================================================
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#---------------------------------------
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# Create revised mutation_info_column
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#---------------------------------------
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gene_LF2['dst_mode'].value_counts()
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gene_LF2[drug].value_counts()
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# note this is overriding, since downstream depends on it
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# make a copy you if you need to keep that
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gene_LF2['mutation_info_labels_orig'] = gene_LF2['mutation_info_labels']
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gene_LF2['mutation_info_labels'] = gene_LF2['dst_mode'].map({1: 'DM'
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, 0: 'OM'})
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gene_LF2['mutation_info_labels_orig'].value_counts()
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gene_LF2['mutation_info_labels'].value_counts()
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#==============================================================================
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# sanity check
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if (all(gene_LF2['mutation'] == gene_LF2['mutationinformation'])):
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print('\nPass: Mutationinformation check successful')
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else:
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sys.exit('\nERROR: mutationin cross checks failed. Please check your group_by() aggregate functions')
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# Drop mutation column
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gene_LF2.drop(['mutation'], axis=1, inplace=True)
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#%% subset: equivalent of merged_df3?
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# https://stackoverflow.com/questions/39900061/sort-lists-in-a-pandas-gene_LF2frame-column
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# result = gene_LF2['dst_multimode'].sort_values().apply(lambda x: sorted(x))
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# newdf = pd.gene_LF2Frame({'dst_multimode': Series(list(set(result['a'].apply(tuple))))})
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# newdf.sort_values(by='a')
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# gene_LF2['dst_multimode'].value_counts()
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# gene_LF2.sort_values(['dst_multimode'], ascending=False)
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#gene_LF2_df3 = gene_LF2.drop_duplicates(['mutationinformation'])
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#gene_LF2_df3_v2 = gene_LF2.drop_duplicates(['mutationinformation'])
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#all(gene_LF2_df3 == gene_LF2_df3_v2)
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#%%
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test_data/processing_v2.py
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test_data/processing_v2.py
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Thu Mar 24 15:01:59 2022
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@author: tanu
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"""
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import sys, os
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import pandas as pd
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import numpy as np
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from statistics import mean, median, mode
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from statistics import multimode
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from collections import Counter
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from tidy_split import tidy_split
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#import math
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# https://stackoverflow.com/questions/43321455/pandas-count-null-values-in-a-groupby-function
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# https://stackoverflow.com/questions/33457191/python-pandas-dataframe-fill-nans-with-a-conditional-mean
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# round up
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# int(math.ceil(mean(foo)))
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# https://stackoverflow.com/questions/33457191/python-pandas-dataframe-fill-nans-with-a-conditional-mean
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# https://stackoverflow.com/questions/37189878/pandas-add-column-to-groupby-dataframe
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# https://stackoverflow.com/questions/43847520/how-to-get-the-distinct-count-of-values-in-a-python-pandas-dataframe
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#%% Read data and formatting
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drug = "pyrazinamide"
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data = pd.read_csv("/home/tanu/git/ML_AI_training/test_data/sample_data.csv")
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data.columns
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data.head()
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#%% Quick checks: Lineage and sample count for each mutation
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data['id'].nunique()
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data['mutationinformation'].nunique()
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total_id_ucount = data['id'].nunique()
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total_id_ucount
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data.groupby('mutationinformation')['lineage'].size()
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data.groupby('mutationinformation')['lineage_corrupt'].size()
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data.groupby('mutationinformation')['id'].size()
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data.groupby('mutationinformation')['lineage'].value_counts()
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data.groupby('mutationinformation')['lineage'].nunique()
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#%% id count: add all id ids and count of unique ids per mutation
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data['id_list'] = data['mutationinformation'].map(data.groupby('mutationinformation')['id'].apply(list))
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data['id_ucount'] = data['mutationinformation'].map(data.groupby('mutationinformation')['id'].nunique())
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data[['mutationinformation', 'id', 'id_list', 'id_ucount']]
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#%% Lineages: add all lineages and count of unique lineages per mutation
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# Lineages good: lineage column has only a single lineage for each mutationinformation
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data['lineage']
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data['lineage_list'] = data['mutationinformation'].map(data.groupby('mutationinformation')['lineage'].apply(list))
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data['lineage_ucount'] = data['mutationinformation'].map(data.groupby('mutationinformation')['lineage'].nunique())
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data[['mutationinformation', 'lineage', 'lineage_list', 'lineage_ucount']]
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# Lineage corrupt: lineage column has only multiple lineages for each mutationinformation separated by ';'
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data['lineage_corrupt']
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# split using tidy_split()
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data_split = tidy_split(data, 'lineage_corrupt', sep = ';')
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# remove leading white space else these are counted as distinct mutations as well
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#data_split['lineage_corrupt'] = data_split['lineage_corrupt'].str.lstrip()
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data_split['lineage_corrupt'] = data_split['lineage_corrupt'].str.strip()
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data_split.head()
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data_split['lineage_corrupt_list'] = data_split['mutationinformation'].map(data_split.groupby('mutationinformation')['lineage_corrupt'].apply(list))
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data_split['lineage_corrupt_ucount'] = data_split['mutationinformation'].map(data_split.groupby('mutationinformation')['lineage_corrupt'].nunique())
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data_split[['mutationinformation', 'lineage_corrupt_list', 'lineage_corrupt_ucount']]
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data_split[['mutationinformation', 'lineage_ucount', 'lineage_corrupt_ucount']]
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#%% AF: calculate AF for each mutation
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#1) calculate no. of unique ids
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data['id_ucount']/total_id_ucount
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#%% DM OM labels
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# COPY mutation_info_labels column
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data['mutation_info_labels_orig'] = data['mutation_info_labels']
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# Convert DM/OM labels to numeric
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dm_om_map = {'DM': 1, 'OM': 0} # pnca, OM is minority, other genes: DM is minority
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data['dm_om_numeric'] = data['mutation_info_labels'].map(dm_om_map)
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# sanity check
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data['dm_om_numeric'].value_counts()
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data['mutation_info_labels'].value_counts()
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# Convert drtype column to numeric
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drtype_map = {'XDR': 5
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, 'Pre-XDR': 4
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, 'MDR': 3
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, 'Pre-MDR': 2
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, 'Other': 1
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, 'Sensitive': 0}
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data['drtype_numeric'] = data['drtype'].map(drtype_map)
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# COPY dst column
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data['dst'] = data[drug] # to allow cross checking
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data['dst_multimode'] = data[drug]
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# sanity check
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data[drug].value_counts()
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data['dst_multimode'].value_counts()
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data[drug].isnull().sum()
|
||||||
|
data['dst_multimode'].isnull().sum()
|
||||||
|
|
||||||
|
data['dst_multimode']
|
||||||
|
|
||||||
|
data['mutationinformation'].value_counts()
|
||||||
|
data[drug].isnull().groupby(data['mutationinformation']).sum()
|
||||||
|
|
||||||
|
# GOAL is to populate na in the dst column from the count of the dm_om_numeric column
|
||||||
|
data['dst_multimode'].isnull().groupby(data['mutationinformation']).sum()
|
||||||
|
|
||||||
|
# COPY mutationinformation for sanity check
|
||||||
|
data['mutation'] = data['mutationinformation']
|
||||||
|
|
||||||
|
#%% POC continued: Test getting mode
|
||||||
|
#data.groupby('mutationinformation')['dm_om_numeric'].mode()
|
||||||
|
data.groupby('mutationinformation')['dm_om_numeric'].agg(mode)
|
||||||
|
data.groupby('mutationinformation')['dm_om_numeric'].agg(multimode)
|
||||||
|
foo = data.groupby('mutationinformation')['dm_om_numeric'].agg(multimode)
|
||||||
|
foo
|
||||||
|
foo = foo.to_frame()
|
||||||
|
foo['dm_om_numeric'].apply(lambda x: max(x))# returns nan
|
||||||
|
foo['dm_om_numeric'].apply(lambda x: np.nanmax(x))
|
||||||
|
#foo.assign(dst_mode = lambda x: (x['dst']))
|
||||||
|
foo['multimode_extract'] = foo['dm_om_numeric'].apply(lambda x: max(x))
|
||||||
|
foo['multimode_extract']
|
||||||
|
#%% Recalculating columns [dst, drtype and mutation_info_labels]: SET Index as 'mutationinformation'
|
||||||
|
data2 = data.copy()
|
||||||
|
# Reset index as it allows the groupby expression to directly map
|
||||||
|
data2 = data2.set_index(['mutationinformation'])
|
||||||
|
#%% Recalculating dst: my data
|
||||||
|
#------------------------------
|
||||||
|
# Revised dst: max(multimode)
|
||||||
|
#------------------------------
|
||||||
|
# For each mutation, generate the revised dst which is the mode of dm_om_numeric
|
||||||
|
# PROBLEM: Returns the smallest of the two when bimodal, and fails when all equally likely
|
||||||
|
# SOLUTION: Using max of the 'dst_noNA' column
|
||||||
|
#data2.groupby('mutationinformation')['dm_om_numeric'].agg(multimode)
|
||||||
|
|
||||||
|
# Get multimode for dm_om_numeric column
|
||||||
|
dm_om_multimode = data2.groupby('mutationinformation')['dm_om_numeric'].agg(multimode)
|
||||||
|
dm_om_multimode
|
||||||
|
|
||||||
|
# Fill using multimode ONLY where NA in dst_multimode column
|
||||||
|
#data2['dst_multimode'] = data2['dst_multimode'].fillna(dm_om_multimode)
|
||||||
|
data2['dst_multimode'] = data2['dst_multimode'].fillna(dm_om_multimode)
|
||||||
|
|
||||||
|
# data2['dst_multimode']
|
||||||
|
|
||||||
|
# Now get the max from multimode
|
||||||
|
data2['dst_noNA'] = data2['dst_multimode'].apply(lambda x: np.nanmax(x))
|
||||||
|
print(data2)
|
||||||
|
|
||||||
|
# Finally created a revised dst with the max from the multimode
|
||||||
|
data2['dst_mode'] = data2.groupby('mutationinformation')['dst_noNA'].max()
|
||||||
|
#==============================================================================
|
||||||
|
#%% Recalculating drtype: my data
|
||||||
|
#--------------------------------
|
||||||
|
# drtype: ALL values:
|
||||||
|
# numeric and names in an array
|
||||||
|
#--------------------------------
|
||||||
|
data2['drtype_all_vals'] = data2['drtype_numeric']
|
||||||
|
data2['drtype_all_names'] = data2['drtype']
|
||||||
|
|
||||||
|
# example: https://stackoverflow.com/questions/55125680/pandas-get-all-groupby-values-in-an-array
|
||||||
|
# print(df.groupby('key').data.apply(list).reset_index()) # my use case, don't need the reset_index()
|
||||||
|
data2['drtype_all_vals'] = data2.groupby('mutationinformation').drtype_all_vals.apply(list)
|
||||||
|
data2['drtype_all_names'] = data2.groupby('mutationinformation').drtype_all_names.apply(list)
|
||||||
|
|
||||||
|
#---------------------------------
|
||||||
|
# Revised drtype: max(Multimode)
|
||||||
|
#--------------------------------
|
||||||
|
data2['drtype_multimode'] = data2.groupby(['mutationinformation'])['drtype_numeric'].agg(multimode)
|
||||||
|
data2['drtype_multimode']
|
||||||
|
|
||||||
|
# Now get the max from multimode
|
||||||
|
data2['drtype_mode'] = data2['drtype_multimode'].apply(lambda x: np.nanmax(x))
|
||||||
|
data2.head()
|
||||||
|
|
||||||
|
#----------------------
|
||||||
|
# Revised drtype: Max
|
||||||
|
#----------------------
|
||||||
|
data2.head()
|
||||||
|
data2['drtype_max'] = data2.groupby(['mutationinformation'])['drtype_numeric'].max()
|
||||||
|
#data2 = data2.reset_index()
|
||||||
|
data2.head()
|
||||||
|
|
||||||
|
#%% Finally reset index
|
||||||
|
data2 = data2.reset_index()
|
||||||
|
#==============================================================================
|
||||||
|
#---------------------------------------
|
||||||
|
# Create revised mutation_info_column
|
||||||
|
#---------------------------------------
|
||||||
|
data2['dst_mode'].value_counts()
|
||||||
|
data2[drug].value_counts()
|
||||||
|
|
||||||
|
# note this is overriding, since downstream depends on it
|
||||||
|
# make a copy you if you need to keep that
|
||||||
|
data2['mutation_info_labels_orig'] = data2['mutation_info_labels']
|
||||||
|
data2['mutation_info_labels'] = data2['dst_mode'].map({1: 'DM'
|
||||||
|
, 0: 'OM'})
|
||||||
|
data2['mutation_info_labels_orig'].value_counts()
|
||||||
|
data2['mutation_info_labels'].value_counts()
|
||||||
|
#==============================================================================
|
||||||
|
# sanity check
|
||||||
|
if (all(data2['mutation'] == data2['mutationinformation'])):
|
||||||
|
print('\nPass: Mutationinformation check successful')
|
||||||
|
else:
|
||||||
|
sys.exit('\nERROR: mutationin cross checks failed. Please check your group_by() aggregate functions')
|
||||||
|
|
||||||
|
# Drop mutation column
|
||||||
|
data2.drop(['mutation'], axis=1, inplace=True)
|
||||||
|
#%% subset: equivalent of merged_df3?
|
||||||
|
# https://stackoverflow.com/questions/39900061/sort-lists-in-a-pandas-dataframe-column
|
||||||
|
|
||||||
|
# result = data2['dst_multimode'].sort_values().apply(lambda x: sorted(x))
|
||||||
|
# newdf = pd.DataFrame({'dst_multimode': Series(list(set(result['a'].apply(tuple))))})
|
||||||
|
# newdf.sort_values(by='a')
|
||||||
|
|
||||||
|
# data2['dst_multimode'].value_counts()
|
||||||
|
# data2.sort_values(['dst_multimode'], ascending=False)
|
||||||
|
|
||||||
|
#data_df3 = data2.drop_duplicates(['mutationinformation'])
|
||||||
|
#data_df3_v2 = data2.drop_duplicates(['mutationinformation'])
|
||||||
|
#all(data_df3 == data_df3_v2)
|
||||||
|
#%%
|
||||||
BIN
test_data/sample_data_pivot.ods
Normal file
BIN
test_data/sample_data_pivot.ods
Normal file
Binary file not shown.
21
test_data/snippet_res_pnca.py
Normal file
21
test_data/snippet_res_pnca.py
Normal file
|
|
@ -0,0 +1,21 @@
|
||||||
|
#!/usr/bin/env python3
|
||||||
|
# -*- coding: utf-8 -*-
|
||||||
|
"""
|
||||||
|
Created on Thu Apr 21 14:54:26 2022
|
||||||
|
|
||||||
|
@author: tanu
|
||||||
|
"""
|
||||||
|
RESULTS:
|
||||||
|
Total WT in dr_muts_col: 30761
|
||||||
|
Total matches of pncA SNP matches in dr_mutations_pyrazinamide : 3973
|
||||||
|
Total samples with > 1 pncA nsSNPs in dr_muts_col: 73
|
||||||
|
Total matches of UNIQUE pncA SNP matches in dr_mutations_pyrazinamide : 227
|
||||||
|
=================================================================RESULTS:
|
||||||
|
Total WT in other_muts_col: 31653
|
||||||
|
Total matches of pncA SNP matches in other_mutations_pyrazinamide : 943
|
||||||
|
Total samples with > 1 pncA nsSNPs in other_muts_col: 14
|
||||||
|
Total matches of UNIQUE pncA SNP matches in other_mutations_pyrazinamide : 200
|
||||||
|
=================================================================
|
||||||
|
|
||||||
|
# First copy index colum
|
||||||
|
# then use the Vcounts analogy for counts
|
||||||
Loading…
Add table
Add a link
Reference in a new issue