combined and output all ors
This commit is contained in:
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d8b272b0ae
commit
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2 changed files with 185 additions and 144 deletions
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@ -34,18 +34,19 @@ from reference_dict import my_aa_dict # CHECK DIR STRUC THERE!
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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', default = None) # case sensitive
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arg_parser.add_argument('-d', '--drug', help = 'drug name', default = 'pyrazinamide')
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arg_parser.add_argument('-g', '--gene', help = 'gene name', default = 'pncA') # case sensitive
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args = arg_parser.parse_args()
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#=======================================================================
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#%% variable assignment: input and output
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drug = 'pyrazinamide'
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gene = 'pncA'
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gene_match = gene + '_p.'
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#drug = 'pyrazinamide'
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#gene = 'pncA'
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#gene_match = gene + '_p.'
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# cmd variables
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#drug = args.drug
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#gene = args.gene
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drug = args.drug
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gene = args.gene
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gene_match = gene + '_p.'
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#==========
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# dir
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@ -57,9 +58,7 @@ outdir = datadir + '/' + drug + '/' + 'output'
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# input
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#=======
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in_filename_afor = gene.lower() + '_af_or.csv'
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# FIXME
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in_filename_afor_kin = gene.lower() + '_af_or_kinship.csv'
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# needs to contain OR. it only has beta!
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infile1 = outdir + '/' + in_filename_afor
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infile2 = outdir + '/' + in_filename_afor_kin
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@ -78,7 +77,7 @@ print('Output file:', outfile
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, '\n===================================================================')
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del(in_filename_afor, in_filename_afor_kin, outfile, datadir, outdir)
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del(in_filename_afor, in_filename_afor_kin, datadir, outdir)
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#%% end of variable assignment for input and output files
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#=======================================================================
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#%% format mutations
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@ -169,12 +168,14 @@ print(ndiff1)
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ndiff2 = afor_kin_df_nrows - afor_kin_df['mutationinformation'].isin(afor_df['mutationinformation']).sum()
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print(ndiff2)
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#%% combining dfs
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# Define join type
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#my_join = 'inner'
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#my_join = 'right'
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##my_join = 'left'
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#my_join = 'left'
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my_join = 'outer'
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fail = False
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# sanity check: how many muts from afor_kin_df are in afor_df. should be a complete subset
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if ndiff2 == 0:
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print('PASS: all muts in afor_kin_df are present in afor_df'
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@ -182,64 +183,31 @@ if ndiff2 == 0:
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combined_df = pd.merge(afor_df, afor_kin_df, on = merging_cols, how = my_join)
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if my_join == 'outer':
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if my_join == ('outer' or 'left') :
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print('combing with:', my_join)
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expected_rows = afor_df_nrows + ndiff1
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expected_cols = (afor_df_ncols + afor_kin_df_ncols) - ncommon_cols
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if len(combined_df) == expected_rows and len(combined_df.columns) == expected_cols:
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print('PASS: successfully combined dfs with:', my_join, 'join')
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else:
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print('FAIL: ', my_join, 'join')
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print('\nExpected no. of rows:', expected_rows
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, '\nGot:', len(combined_df)
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, '\nExpected no. of cols:', expected_cols
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, '\nGot:', len(combined_df.columns))
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elif my_join == 'inner':
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if my_join == ('inner' or 'right'):
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print('combing with:', my_join)
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expected_rows = afor_kin_df_nrows
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expected_cols = (afor_df_ncols + afor_kin_df_ncols) - ncommon_cols
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if len(combined_df) == expected_rows and len(combined_df.columns) == expected_cols:
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print('PASS: successfully combined dfs with:', my_join, 'join')
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else:
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print('FAIL: ', my_join, 'join')
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print('\nExpected no. of rows:', expected_rows
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, '\nGot:', len(combined_df)
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, '\nExpected no. of cols:', expected_cols
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, '\nGot:', len(combined_df.columns))
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elif my_join == 'left':
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expected_rows = afor_df_nrows + ndiff1
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expected_cols = (afor_df_ncols + afor_kin_df_ncols) - ncommon_cols
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if len(combined_df) == expected_rows and len(combined_df.columns) == expected_cols:
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print('PASS: successfully combined dfs with:', my_join, 'join')
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else:
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print('FAIL: ', my_join, 'join')
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print('\nExpected no. of rows:', expected_rows
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, '\nGot:', len(combined_df)
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, '\nExpected no. of cols:', expected_cols
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, '\nGot:', len(combined_df.columns))
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elif my_join == 'right':
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expected_rows = afor_kin_df_nrows
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expected_cols = (afor_df_ncols + afor_kin_df_ncols) - ncommon_cols
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if len(combined_df) == expected_rows and len(combined_df.columns) == expected_cols:
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print('PASS: successfully combined dfs with:', my_join, 'join')
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else:
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print('FAIL: ', my_join, 'join')
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print('\nExpected no. of rows:', expected_rows
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, '\nGot:', len(combined_df)
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, '\nExpected no. of cols:', expected_cols
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, '\nGot:', len(combined_df.columns))
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expected_cols = afor_df_ncols + afor_kin_df_ncols - ncommon_cols
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if len(combined_df) == expected_rows and len(combined_df.columns) == expected_cols:
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print('PASS: successfully combined dfs with:', my_join, 'join')
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else:
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print('FAIL: failed to combine dfs, expected rows and cols not matched')
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print('FAIL: combined_df\'s expected rows and cols not matched')
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fail = True # BAD practice! just a placeholder to avoid code duplication
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print('\nExpected no. of rows:', expected_rows
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, '\nGot:', len(combined_df)
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, '\nExpected no. of cols:', expected_cols
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, '\nGot:', len(combined_df.columns))
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if fail:
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sys.exit('ERROR: combined_df may be incorrectly combined')
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else:
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print('FAIL: numbers mismatch, mutations present in afor_kin_df but not in afor_df')
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sys.exit('ERROR: Not all mutations in the kinship_df are present in the df with other ORs')
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#%% check duplicate cols: ones containing suffix '_x' or '_y'
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# should only be position
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@ -256,78 +224,73 @@ combined_or_df['position'].head()
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# recheck
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foo = combined_or_df.filter(regex = r'.*_x|_y', axis = 1)
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print(foo.columns) # should only be position
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print(foo.columns) # should only be empty
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combined_or_df['af'].head()
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combined_or_df.rename(columns = {'af': 'af_kin'}, inplace = True)
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combined_or_df['af_kin']
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#%% calculate OR for kinship
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combined_or_df['or_kin'] = np.exp(combined_or_df['beta'])
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#%% rearraging columns
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print('Dim of df prefromatting:', combined_or_df.shape)
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# drop duplicate columns
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#if combined_or_df['alternate_allele'].equals(combined_or_df['alt_allele0']):
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# combined_or_df.drop('alternate_allele', axis = 1, inplace = True)
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combined_or_df2 = combined_or_df.T.drop_duplicates().T# changes dtypes in cols
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dup_cols = set(combined_or_df.columns).difference(combined_or_df2.columns)
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#tot_diff is equal to n_diff
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# drop some not required cols
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combined_or_df.drop(list(dup_cols), axis = 1, inplace = True)
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print(combined_or_df.columns)
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combined_or_df.drop(['chromosome_text', 'chr', 'symbol', '_merge', ], axis = 1, inplace = True)
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combined_or_df.rename(columns = {'ref_allele1': 'reference_allele'}, inplace = True)
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print(combined_or_df.columns)
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#%% reorder columns
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#https://stackoverflow.com/questions/13148429/how-to-change-the-order-of-dataframe-columns
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# check af: curiosity
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# setting column's order
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output_df = combined_or_df[['mutation', 'wild_type', 'position', 'mutant_type', 'mutationinformation'
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, 'chr_num_allele', 'ref_allele', 'alt_allele'
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, 'mut_info', 'mut_type', 'gene_id', 'gene_number', 'mut_region'
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, 'reference_allele', 'alternate_allele', 'chromosome_number'
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, 'afs', 'af_kin', 'ors_logistic', 'ors_chi_cus', 'or_kin', 'ors_fisher'
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, 'pvals_logistic', 'pvals_fisher', 'p_wald', 'ci_lb_fisher', 'ci_ub_fisher'
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, 'beta', 'se', 'logl_H1', 'l_remle','stat_chi', 'pvals_chi', 'n_diff' , 'n_miss']]
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output_df = combined_or_df[['mutation',
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'mutationinformation',
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'wild_type',
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'position',
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'mutant_type',
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'chr_num_allele',
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'ref_allele',
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'alt_allele',
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'mut_info',
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'mut_type',
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'gene_id',
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'gene_number',
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'mut_region',
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'reference_allele',
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'alternate_allele',
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'chromosome_number',
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'af',
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'af_kin',
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'or_kin',
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'or_logistic',
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'or_mychisq',
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'est_chisq',
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'or_fisher',
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'ci_low_logistic',
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'ci_hi_logistic',
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'ci_low_fisher',
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'ci_hi_fisher',
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'pwald_kin',
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'pval_logistic',
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'pval_fisher',
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'pval_chisq',
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'beta_logistic',
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'beta_kin',
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'se_logistic',
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'se_kin',
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'zval_logistic',
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'logl_H1_kin',
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'l_remle_kin',
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'n_diff',
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'tot_diff',
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'n_miss']]
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#%% output combined or df
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#===============
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# writing file
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#===============
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print('Writing file...')
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#combined_or_df.to_csv(outfile, header = True, index = False)
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output_df.to_csv(outfile, header = True, index = False)
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print('Finished writing file:', outfile
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, '\nNo. of rows:', len(combined_or_df)
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, '\nNo. of cols:', len(combined_or_df.columns)
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, '\n=========================================================')
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#%% practice
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df = pd.DataFrame()
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column_names = ['x','y','z','mean']
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for col in column_names:
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df[col] = np.random.randint(0,100, size=10000)
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df.head()
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# drop duplicate col with dup values not necessarily colnames
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df['xdup'] = df['x']
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df
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df = df.T.drop_duplicates().T
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#import math
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math.exp(0)
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df['expX'] = np.exp(df['x']) # math doesn't understand series dtype
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df
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#%%
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# sanity check after rearranging
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if combined_or_df.shape == output_df.shape and set(combined_or_df.columns) == set(output_df.columns):
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print('PASS: Successfully formatted df with rearranged columns')
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else:
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sys.exit('FAIL: something went wrong when rearranging columns!')
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#%% write file
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print('\n====================================================================='
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, '\nWriting output file:\n', outfile
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, '\nNo.of rows:', len(output_df)
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, '\nNo. of cols:', len(output_df.columns))
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output_df.to_csv(outfile, index = False)
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@ -14,7 +14,7 @@ Created on Wed Jun 10 11:13:49 2020
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#%% specify dirs
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import os, sys
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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 re
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import argparse
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@ -26,8 +26,8 @@ from find_missense import find_missense
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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) # case sensitive
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arg_parser.add_argument('-d', '--drug', help = 'drug name', default = 'pyrazinamide')
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arg_parser.add_argument('-g', '--gene', help = 'gene name (case sensitive)', default = 'pncA') # case sensitive
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arg_parser.add_argument('-s', '--start_coord', help = 'start of coding region (cds) of gene', default = 2288681) # pnca cds
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arg_parser.add_argument('-e', '--end_coord', help = 'end of coding region (cds) of gene', default = 2289241) # pnca cds
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@ -37,6 +37,8 @@ args = arg_parser.parse_args()
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#%% variables
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#gene = 'pncA'
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#drug = 'pyrazinamide'
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#start_cds = 2288681
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#end_cds = 2289241
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# cmd variables
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gene = args.gene
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@ -94,7 +96,7 @@ or_df.columns
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info_df2 = pd.read_csv(gene_info, sep = '\t', header = 0) #303, 10
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mis_mut_cover = (info_df2['chromosome_number'].nunique()/info_df2['chromosome_number'].count()) * 100
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print('*****RESULT*****'
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, '\nPercentage of missense mut in pncA:', mis_mut_cover
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, '\nPercentage of MISsense mut in pncA:', mis_mut_cover
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, '\n*****RESULT*****') #65.7%
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# large file
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@ -117,8 +119,6 @@ genomic_pos_min = info_df['chromosome_number'].min()
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genomic_pos_max = info_df['chromosome_number'].max()
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# genomic coord for pnca coding region
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#start_cds = 2288681
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#end_cds = 2289241
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cds_len = (end_cds-start_cds) + 1
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pred_prot_len = (cds_len/3) - 1
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@ -134,6 +134,7 @@ if genomic_pos_min <= start_cds and genomic_pos_max >= end_cds:
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print ('PASS: coding region for gene included in snp_info.txt')
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else:
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print('FAIL: coding region for gene not included in info file snp_info.txt')
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sys.exit('ERROR: coding region of gene not included in the info file')
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#%% Extracting ref allele and alt allele as single letters
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# info_df has some of these params as more than a single letter, which means that
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@ -162,7 +163,7 @@ del(orig_len, ncols_add)
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# check dtypes
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or_df.dtypes
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info_df.dtypes
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or_df.info()
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#or_df.info()
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# pandas documentation where it mentions: "Pandas uses the object dtype for storing strings"
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# check how many unique chr_num in info_df are in or_df
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@ -175,23 +176,22 @@ or_df['chromosome_number'].isin(genomic_pos_df['chr_pos']).sum() #182
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if or_df['chromosome_number'].isin(genomic_pos_df['chr_pos']).sum() == len(or_df):
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print('PASS: all genomic locs in or_df have meta datain info.txt')
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else:
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print('FAIL: some genomic locs or_df chr number DO NOT have meta data in snp_info.txt')
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sys.exit('FAIL: some genomic locs or_df chr number DO NOT have meta data in snp_info.txt')
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#%% Perform merge
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#join_type = 'inner'
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#join_type = 'outer'
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join_type = 'left'
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#join_type = 'right'
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#my_join = 'inner'
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#my_join = 'outer'
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my_join = 'left'
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#my_join = 'right'
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#dfm1 = pd.merge(or_df, info_df, on ='chromosome_number', how = join_type, indicator = True) # not unique!
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dfm1 = pd.merge(or_df, info_df, on = ['chromosome_number', 'ref_allele', 'alt_allele'], how = join_type, indicator = True)
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#dfm1 = pd.merge(or_df, info_df, on ='chromosome_number', how = my_join, indicator = True) # not unique!
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dfm1 = pd.merge(or_df, info_df, on = ['chromosome_number', 'ref_allele', 'alt_allele'], how = my_join, indicator = True)
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dfm1['_merge'].value_counts()
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# count no. of missense mutations ONLY
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dfm1.snp_info.str.count(r'(missense.*)').sum()
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dfm2 = pd.merge(or_df, info_df2, on = ['chromosome_number', 'ref_allele', 'alt_allele'], how = join_type, indicator = True)
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dfm2 = pd.merge(or_df, info_df2, on = ['chromosome_number', 'ref_allele', 'alt_allele'], how = my_join, indicator = True)
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dfm2['_merge'].value_counts()
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# count no. of nan
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@ -241,12 +241,90 @@ else:
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, '\nGot no. of cols:', len(dfm2_mis.columns))
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sys.exit()
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#%% formatting data for output
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print('no of cols preformatting data:', len(dfm2_mis.columns))
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#1) Add column: OR for kinship calculated from beta coeff
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print('converting beta coeff to OR by exponent function\n:'
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, dfm2_mis['beta'].head())
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dfm2_mis['or_kin'] = np.exp(dfm2_mis['beta'])
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print(dfm2_mis['or_kin'].head())
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#2) rename af column
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dfm2_mis.rename(columns = {'af': 'af_kin'
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, 'beta': 'beta_kin'
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, 'p_wald': 'pwald_kin'
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, 'se': 'se_kin', 'logl_H1': 'logl_H1_kin'
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, 'l_remle': 'l_remle_kin'}, inplace = True)
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#3) drop some not required cols (including duplicate if you want)
|
||||
|
||||
#3a) drop duplicate columns
|
||||
dfm2_mis2 = dfm2_mis.T.drop_duplicates().T #changes dtypes in cols, so not used
|
||||
dup_cols = set(dfm2_mis.columns).difference(dfm2_mis2.columns)
|
||||
print('Duplicate columns identified:', dup_cols)
|
||||
dup_cols = {'alt_allele0', 'ps'} # didn't want to remove tot_diff
|
||||
|
||||
print('removing duplicate columns: kept one of the dup_cols i.e tot_diff')
|
||||
dfm2_mis.drop(list(dup_cols), axis = 1, inplace = True)
|
||||
print(dfm2_mis.columns)
|
||||
|
||||
#3b) other not useful columns
|
||||
dfm2_mis.drop(['chromosome_text', 'chr', 'symbol', '_merge', ], axis = 1, inplace = True)
|
||||
dfm2_mis.rename(columns = {'ref_allele1': 'reference_allele'}, inplace = True)
|
||||
|
||||
print(dfm2_mis.columns)
|
||||
|
||||
#4) reorder columns
|
||||
orkin_linked = dfm2_mis[['mutationinformation',
|
||||
'wild_type',
|
||||
'position',
|
||||
'mutant_type',
|
||||
'chr_num_allele',
|
||||
'ref_allele',
|
||||
'alt_allele',
|
||||
'mut_info',
|
||||
'mut_type',
|
||||
'gene_id',
|
||||
'gene_number',
|
||||
'mut_region',
|
||||
'reference_allele',
|
||||
'alternate_allele',
|
||||
'chromosome_number',
|
||||
#'afs
|
||||
'af_kin',
|
||||
'or_kin',
|
||||
# 'ors_logistic',
|
||||
# 'ors_chi_cus',
|
||||
# 'ors_fisher',
|
||||
'pwald_kin',
|
||||
# 'pvals_logistic',
|
||||
# 'pvals_fisher',
|
||||
# 'ci_lb_fisher',
|
||||
# 'ci_ub_fisher' ,
|
||||
'beta_kin',
|
||||
'se_kin',
|
||||
'logl_H1_kin',
|
||||
'l_remle_kin',
|
||||
# 'stat_chi',
|
||||
# 'pvals_chi',
|
||||
'n_diff',
|
||||
'tot_diff',
|
||||
'n_miss']]
|
||||
|
||||
|
||||
# sanity check after reassigning columns
|
||||
if orkin_linked.shape == dfm2_mis.shape and set(orkin_linked.columns) == set(dfm2_mis.columns):
|
||||
print('PASS: Successfully formatted df with rearranged columns')
|
||||
else:
|
||||
sys.exit('FAIL: something went wrong when rearranging columns!')
|
||||
|
||||
#%% write file
|
||||
print('Writing output file:\n', outfile_or_kin
|
||||
print('\n====================================================================='
|
||||
, '\nWriting output file:\n', outfile_or_kin
|
||||
, '\nNo.of rows:', len(dfm2_mis)
|
||||
, '\nNo. of cols:', len(dfm2_mis.columns))
|
||||
dfm2_mis.to_csv(outfile_or_kin, index = False)
|
||||
orkin_linked.to_csv(outfile_or_kin, index = False)
|
||||
|
||||
#%% diff b/w allele0 and 1: or_df
|
||||
#https://stackoverflow.com/questions/40348541/pandas-diff-with-string
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue