added output file for checking
This commit is contained in:
parent
dcd9a985ec
commit
2d8cb01cb7
2 changed files with 38 additions and 352 deletions
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@ -52,7 +52,7 @@ Created on Tue Aug 6 12:56:03 2019
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import os, sys
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import os, sys
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import re
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import re
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import pandas as pd
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import pandas as pd
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#import numpy as np
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import numpy as np
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import argparse
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import argparse
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#=======================================================================
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#=======================================================================
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#%% homdir and curr dir and local imports
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#%% homdir and curr dir and local imports
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@ -68,18 +68,17 @@ from tidy_split import tidy_split
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#=======================================================================
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#=======================================================================
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#%% command line args
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#%% command line args
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arg_parser = argparse.ArgumentParser()
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arg_parser = argparse.ArgumentParser()
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arg_parser.add_argument('-d', '--drug', help='drug name', default = None)
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arg_parser.add_argument('-d', '--drug', help='drug name (case sensitive)', default = None)
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arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = None)
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arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = None)
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args = arg_parser.parse_args()
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args = arg_parser.parse_args()
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#=======================================================================
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#=======================================================================
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#%% variable assignment: input and output paths & filenames
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#%% variable assignment: input and output paths & filenames
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#drug = args.drug
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drug = args.drug
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#gene = args.gene
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gene = args.gene
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drug = 'pyrazinamide'
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#drug = 'pyrazinamide'
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gene = 'pncA'
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#gene = 'pncA'
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gene_match = gene + '_p.'
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gene_match = gene + '_p.'
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print('mut pattern for gene', gene, ':', gene_match)
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print('mut pattern for gene', gene, ':', gene_match)
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@ -99,6 +98,7 @@ print('position regex:', pos_regex)
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# building cols to extract
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# building cols to extract
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dr_muts_col = 'dr_mutations_' + drug
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dr_muts_col = 'dr_mutations_' + drug
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other_muts_col = 'other_mutations_' + drug
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other_muts_col = 'other_mutations_' + drug
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resistance_col = 'drtype'
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print('Extracting columns based on variables:\n'
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print('Extracting columns based on variables:\n'
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, drug
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, drug
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@ -106,6 +106,8 @@ print('Extracting columns based on variables:\n'
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, dr_muts_col
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, dr_muts_col
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, '\n'
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, '\n'
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, other_muts_col
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, other_muts_col
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, '\n'
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, resistance_col
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, '\n===============================================================')
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, '\n===============================================================')
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#=======================================================================
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#=======================================================================
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#%% input and output dirs and files
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#%% input and output dirs and files
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@ -120,7 +122,7 @@ outdir = datadir + '/' + drug + '/' + 'output'
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# input
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# input
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#=======
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#=======
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#in_filename_master_master = 'original_tanushree_data_v2.csv' #19k
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#in_filename_master_master = 'original_tanushree_data_v2.csv' #19k
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in_filename_master = 'mtb_gwas_meta_v3.csv' #33k
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in_filename_master = 'mtb_gwas_meta_v5.csv' #34k
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infile_master = datadir + '/' + in_filename_master
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infile_master = datadir + '/' + in_filename_master
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print('Input file: ', infile_master
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print('Input file: ', infile_master
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, '\n============================================================')
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, '\n============================================================')
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@ -147,33 +149,37 @@ if in_filename_master == 'original_tanushree_data_v2.csv':
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, 'country'
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, 'country'
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, 'lineage'
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, 'lineage'
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, 'sublineage'
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, 'sublineage'
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, 'drtype' #19k only
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, 'drtype'
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, drug
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, drug
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, dr_muts_col
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, dr_muts_col
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, other_muts_col]]
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, other_muts_col]]
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if in_filename_master == 'mtb_gwas_meta_v3.csv':
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if in_filename_master == 'mtb_gwas_meta_v5.csv':
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core_cols = ['id'
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core_cols = ['id'
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, 'country'
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, 'sample'
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, 'country2'
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, 'patient_id'
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, 'geographic_source'
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, 'region'
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, 'date'
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, 'strain'
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, 'strain'
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, 'lineage'
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, 'lineage'
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, 'sublineage' #drtype renamed to resistance
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, 'sublineage'
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, 'resistance'
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, 'country'
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, 'country_code'
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, 'geographic_source'
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#, 'region'
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, 'location'
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, 'location'
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, 'host_body_site'
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, 'host_body_site'
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, 'environment_material'
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, 'environment_material'
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, 'host_status'
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, 'host_status'
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, 'host_sex'
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, 'submitted_host_sex'
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, 'hiv_status'
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, 'hiv_status'
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, 'HIV_status'
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, 'HIV_status'
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, 'tissue_type'
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, 'isolation_source']
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, 'isolation_source']
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variable_based_cols = [drug
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variable_based_cols = [drug
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, dr_muts_col
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, dr_muts_col
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, other_muts_col]
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, other_muts_col
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, resistance_col]
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cols_to_extract = core_cols + variable_based_cols
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cols_to_extract = core_cols + variable_based_cols
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print('Extracting', len(cols_to_extract), 'columns from master data')
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print('Extracting', len(cols_to_extract), 'columns from master data')
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@ -193,7 +199,14 @@ print('RESULT: Total samples:', total_samples
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meta_data.isna().sum()
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meta_data.isna().sum()
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print('No. of NAs/column:' + '\n', meta_data.isna().sum()
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print('No. of NAs/column:' + '\n', meta_data.isna().sum()
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, '\n===========================================================')
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, '\n===========================================================')
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#
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#%% Write check file
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check_file = outdir + '/' + gene.lower() + '_gwas.csv'
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meta_data.to_csv(check_file)
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print('Writing subsetted gwas data'
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, '\nFile', check_file
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, '\nDim:', meta_data.shape)
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# glance
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# glance
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#meta_data.head()
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#meta_data.head()
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#total_samples - NA pyrazinamide = ?
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#total_samples - NA pyrazinamide = ?
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@ -203,7 +216,10 @@ print('No. of NAs/column:' + '\n', meta_data.isna().sum()
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# equivalent of table in R
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# equivalent of table in R
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# drug counts: complete samples for OR calcs
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# drug counts: complete samples for OR calcs
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meta_data[drug].value_counts()
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meta_data[drug].value_counts()
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print('RESULT: Sus and Res samples:\n', meta_data[drug].value_counts()
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print('===========================================================\n'
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, 'RESULT: No. of Sus and Res samples:\n', meta_data[drug].value_counts()
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, '\n===========================================================\n'
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, 'RESULT: Percentage of Sus and Res samples:\n', meta_data[drug].value_counts(normalize = True)*100
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, '\n===========================================================')
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, '\n===========================================================')
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#%%
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#%%
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@ -306,7 +322,8 @@ print('Predicting total no. of rows in the curated df:', dr_gene_count + other_g
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, '\n===================================================================')
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, '\n===================================================================')
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expected_rows = dr_gene_count + other_gene_count
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expected_rows = dr_gene_count + other_gene_count
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del(i, id, wt_other, clean_df, na_count, id2_other, count_gene_other, count_wt)
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#del( wt_other, clean_df, i, id, na_count, id2_other, count_gene_other, count_wt)
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del(clean_df, na_count, i, id, wt_other, id2_other, count_gene_other,count_wt )
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#%%
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#%%
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############
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############
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@ -1,331 +0,0 @@
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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 Tue Aug 6 12:56:03 2019
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@author: tanu
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'''
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# FIXME: include error checking to enure you only
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# concentrate on positions that have structural info?
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# FIXME: import dirs.py to get the basic dir paths available
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#=======================================================================
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# TASK:
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#=======================================================================
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#%% load libraries
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import os, sys
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import re
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import pandas as pd
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import numpy as np
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import argparse
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#=======================================================================
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#%% homdir and curr dir and local imports
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homedir = os.path.expanduser('~')
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# set working dir
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os.getcwd()
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os.chdir(homedir + '/git/LSHTM_analysis/scripts')
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os.getcwd()
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# import aa dict
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#from reference_dict import my_aa_dict # CHECK DIR STRUC THERE!
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#from tidy_split import tidy_split
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#=======================================================================
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#%% command line args
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arg_parser = argparse.ArgumentParser()
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arg_parser.add_argument('-d', '--drug', help='drug name', default = None)
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arg_parser.add_argument('-g', '--gene', help='gene name (case sensitive)', default = None)
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args = arg_parser.parse_args()
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#=======================================================================
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#%% variable assignment: input and output paths & filenames
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#drug = args.drug
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#gene = args.gene
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drug = 'pyrazinamide'
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gene = 'pncA'
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gene_match = gene + '_p.'
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print('mut pattern for gene', gene, ':', gene_match)
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nssnp_match = gene_match +'[A-Z]{3}[0-9]+[A-Z]{3}'
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print('nsSNP for gene', gene, ':', nssnp_match)
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wt_regex = gene_match.lower()+'(\w{3})'
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print('wt regex:', wt_regex)
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mut_regex = r'\d+(\w{3})$'
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print('mt regex:', mut_regex)
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pos_regex = r'(\d+)'
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print('position regex:', pos_regex)
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# building cols to extract
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dr_muts_col = 'dr_mutations_' + drug
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other_muts_col = 'other_mutations_' + drug
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dr_type = "resistance"
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print('Extracting columns based on variables:\n'
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, drug
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, '\n'
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, dr_type
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, '\n'
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, dr_muts_col
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, '\n'
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, other_muts_col
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, '\n===============================================================')
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#=======================================================================
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#%% input and output dirs and files
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#=======
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# dirs
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#=======
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datadir = homedir + '/' + 'git/Data'
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indir = datadir + '/' + drug + '/' + 'input'
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outdir = datadir + '/' + drug + '/' + 'output'
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#=======
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# input
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#=======
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#in_filename_master_master = 'original_tanushree_data_v2.csv' #19k
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in_filename_v2 = 'original_tanushree_data_v2.csv' #19k
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infile_master_v2 = datadir + '/' + in_filename_v2
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print('Input file v2: ', infile_master_v2
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, '\n============================================================')
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in_filename_v3 = 'mtb_gwas_meta_v3.csv' #33k
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infile_master_v3 = datadir + '/' + in_filename_v3
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print('Input file v3: ', infile_master_v3
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, '\n============================================================')
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in_filename_v4 = 'mtb_gwas_meta_v4.csv' #34k
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infile_master_v4 = datadir + '/' + in_filename_v4
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print('Input file v4: ', infile_master_v4
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, '\n============================================================')
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in_filename_v5 = 'mtb_gwas_meta_v5.csv' #34k
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infile_master_v5 = datadir + '/' + in_filename_v5
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print('Input file v4: ', infile_master_v5
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, '\n============================================================')
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#=======
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# output
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#=======
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# several output files: in respective sections at the time of outputting files
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print('Output filename: in the respective sections'
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, '\nOutput path: ', outdir
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, '\n=============================================================')
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#%%end of variable assignment for input and output files
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#=======================================================================
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#%% Read input file
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master_data_v2 = pd.read_csv(infile_master_v2, sep = ',', dtype = 'unicode') # ascii
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master_data_v3 = pd.read_csv(infile_master_v3, sep = ',', dtype = 'unicode')
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master_data_v4 = pd.read_csv(infile_master_v4, sep = ',', dtype = 'unicode')
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master_data_v5 = pd.read_csv(infile_master_v5, sep = ',', dtype = 'unicode')
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#DtypeWarning: Columns (48) have mixed types.Specify dtype option on import or set low_memory=False.
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# interactivity=interactivity, compiler=compiler, result=result)
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#==========
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# na_check
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#==========
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#==================================================================
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v2_na = master_data_v2.isna().sum()
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v2_na.name = "v2_na_count"
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v2_na = v2_na.to_frame()
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v2_na['v2_na_percent'] = master_data_v2.isna().mean().round(4)*100
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master_data_v2['drtype'].value_counts()
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master_data_v2['drtype'].value_counts().sum() == len(master_data_v2)
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v2 = master_data_v2[['id'
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, 'country'
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, 'lineage'
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, 'sublineage'
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, 'drtype'
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, drug
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, dr_muts_col
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, other_muts_col]]
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v2.isna().sum()
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print('complete samples v2:', v2['id'].nunique() - v2[drug].isna().sum())
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#==================================================================
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v3_na = master_data_v3.isna().sum()
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v3_na.name = "v3_na_count"
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v3_na = v3_na.to_frame()
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v3_na['v3_na_percent'] = master_data_v3.isna().mean().round(4)*100
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master_data_v3['resistance'].value_counts()
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master_data_v3['resistance'].value_counts().sum() == len(master_data_v3)
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v3 = master_data_v3[['id'
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, 'country'
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, 'lineage'
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, 'sublineage'
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, 'resistance'
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, drug
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, dr_muts_col
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, other_muts_col]]
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v3.isna().sum()
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print('complete samples v3:', v3['id'].nunique() - v3[drug].isna().sum())
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#==================================================================
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v4_na = master_data_v4.isna().sum()
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v4_na.name = "v4_na_count"
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v4_na = v4_na.to_frame()
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v4_na['v4_na_percent'] = master_data_v4.isna().mean().round(4)*100
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v4 = master_data_v4[['id'
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, 'country'
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, 'lineage'
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, 'sublineage'
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, drug
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, dr_muts_col
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, other_muts_col]]
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v4.isna().sum()
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print('complete samples v4:', v4['id'].nunique() - v4[drug].isna().sum())
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#==================================================================
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v5_na = master_data_v5.isna().sum()
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v5_na.name = "v5_na_count"
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v5_na = v5_na.to_frame()
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v5_na['v4_na_percent'] = master_data_v5.isna().mean().round(4)*100
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v5 = master_data_v5[['id'
|
|
||||||
, 'country'
|
|
||||||
, 'lineage'
|
|
||||||
, 'sublineage'
|
|
||||||
, drug
|
|
||||||
, dr_muts_col
|
|
||||||
, other_muts_col]]
|
|
||||||
|
|
||||||
v5.isna().sum()
|
|
||||||
|
|
||||||
print('complete samples v5:', v5['id'].nunique() - v5[drug].isna().sum())
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
#====================================================================
|
|
||||||
# checking ids
|
|
||||||
id_check1 = master_data_v2['id'].isin(master_data_v3['id']).sum()
|
|
||||||
print('No. of 19k dataset (v1) ids in 33k dataset (v2):',id_check1)
|
|
||||||
|
|
||||||
id_check2 = master_data_v2['id'].isin(master_data_v4['id']).sum()
|
|
||||||
print('No. of 19k dataset (v1) ids in 34k dataset (v4):',id_check2)
|
|
||||||
id_check3 = master_data_v4['id'].isin(master_data_v2['id']).sum()
|
|
||||||
print('No. of 19k dataset (v1) ids in 34k dataset (v4):',id_check3)
|
|
||||||
|
|
||||||
id_check4 = master_data_v3['sample_accession'].isin(master_data_v4['sample_accession']).sum()
|
|
||||||
print('No. of 33k dataset (v3) ids in 34k dataset (v3):',id_check4)
|
|
||||||
id_check5 = master_data_v4['sample_accession'].isin(master_data_v3['sample_accession']).sum()
|
|
||||||
print('No. of 34k dataset (v4) ids in 33k dataset (v3):', id_check5)
|
|
||||||
|
|
||||||
master_data_v3['sample_accession'].equals(master_data_v3['accession'])
|
|
||||||
master_data_v3['sample_accession'].isin(master_data_v3['accession']).sum()
|
|
||||||
master_data_v3['accession'].isin(master_data_v3['sample_accession']).sum()
|
|
||||||
|
|
||||||
|
|
||||||
master_data_v4['sample_accession'].equals(master_data_v4['accession'])
|
|
||||||
master_data_v4['sample_accession'].isin(master_data_v4['accession']).sum()
|
|
||||||
master_data_v4['accession'].isin(master_data_v4['sample_accession']).sum()
|
|
||||||
|
|
||||||
#===================================================================
|
|
||||||
|
|
||||||
|
|
||||||
#====================================================================
|
|
||||||
#which v3 cols are NOT IN V4
|
|
||||||
master_data_v3.columns[~master_data_v3.columns.isin(master_data_v4.columns)]
|
|
||||||
|
|
||||||
# which v4 cols ARE NOT in v3
|
|
||||||
master_data_v4.columns[~master_data_v4.columns.isin(master_data_v3.columns)]
|
|
||||||
|
|
||||||
|
|
||||||
# job: I need resistance and region in v4 data from v3
|
|
||||||
# find mergig cols
|
|
||||||
np.intersect1d(master_data_v3.columns, master_data_v4.columns)
|
|
||||||
|
|
||||||
|
|
||||||
master_data_v3['id'].nunique() == len(master_data_v3)
|
|
||||||
master_data_v3['sample_accession'].nunique() == len(master_data_v3)
|
|
||||||
master_data_v3['accession'].nunique() == len(master_data_v3)
|
|
||||||
master_data_v3['run_accession'].nunique() == len(master_data_v3)
|
|
||||||
|
|
||||||
|
|
||||||
master_data_v4['id'].nunique() == len(master_data_v4)
|
|
||||||
master_data_v4['sample_accession'].nunique() == len(master_data_v4)
|
|
||||||
master_data_v4['accession'].nunique() == len(master_data_v4)
|
|
||||||
master_data_v4['run_accession'].nunique() == len(master_data_v4)
|
|
||||||
|
|
||||||
c_v4 = master_data_v4[['id', 'sample', 'sample_accession', 'run_accession', 'accession'
|
|
||||||
, 'location', 'country', 'geographic_source', 'country_code']]
|
|
||||||
c_v4.isna().sum()
|
|
||||||
|
|
||||||
c_v4_ids = master_data_v4[['id', 'sample', 'sample_accession', 'run_accession', 'accession']]
|
|
||||||
c_v4_ids.isna().sum()
|
|
||||||
c_v4_ids.eq(c_v4_ids.iloc[:, 0], axis=0)
|
|
||||||
|
|
||||||
c_v3 = master_data_v3[['id', 'sample_accession', 'run_accession','accession'
|
|
||||||
, 'location', 'country', 'geographic_source', 'region']]
|
|
||||||
c_v3.isna().sum()
|
|
||||||
c_v3_ids = master_data_v3[['id', 'sample_accession', 'run_accession', 'accession']]
|
|
||||||
c_v3_ids.isna().sum()
|
|
||||||
c_v3_ids.eq(c_v3_ids.iloc[:, 0], axis=0)
|
|
||||||
# comment: id, sample, sample_accession and run_accession seem to have no na
|
|
||||||
|
|
||||||
master_data_v4[drug].isna().sum()
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
#%% Write file: mCSM muts
|
|
||||||
|
|
||||||
|
|
||||||
#%% Write file: gene_metadata (i.e gene_LF1)
|
|
||||||
# where each row has UNIQUE mutations NOT unique sample ids
|
|
||||||
out_filename_metadata = gene.lower() + '_metadata.csv'
|
|
||||||
outfile_metadata = outdir + '/' + out_filename_metadata
|
|
||||||
print('Writing file: LF formatted data'
|
|
||||||
, '\nFile:', outfile_metadata
|
|
||||||
, '\n============================================================')
|
|
||||||
|
|
||||||
gene_LF1.to_csv(outfile_metadata, header = True, index = False)
|
|
||||||
print('Finished writing:', outfile_metadata
|
|
||||||
, '\nNo. of rows:', len(gene_LF1)
|
|
||||||
, '\nNo. of cols:', len(gene_LF1.columns)
|
|
||||||
, '\n=============================================================')
|
|
||||||
del(out_filename_metadata)
|
|
||||||
|
|
||||||
#%% write file: mCSM style but with repitions for MSA and logo plots
|
|
||||||
|
|
||||||
print('Writing file: mCSM style muts for msa',
|
|
||||||
'\nFile:', outfile_msa,
|
|
||||||
'\nmutation format (SNP): {WT}<POS>{MUT}',
|
|
||||||
'\nNo.of lines of msa:', len(all_muts_msa))
|
|
||||||
|
|
||||||
all_muts_msa_sorted.to_csv(outfile_msa, header = False, index = False)
|
|
||||||
|
|
||||||
print('Finished writing:', outfile_msa
|
|
||||||
, '\nNo. of rows:', len(all_muts_msa)
|
|
||||||
, '\nNo. of cols:', len(all_muts_msa.columns)
|
|
||||||
, '\n=============================================================')
|
|
||||||
|
|
||||||
del(out_filename_msa)
|
|
||||||
|
|
||||||
Loading…
Add table
Add a link
Reference in a new issue