extracted results for dynamut gid bissection b10_21
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3 changed files with 16 additions and 11 deletions
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@ -21,14 +21,14 @@ from pandas.api.types import is_numeric_dtype
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def format_mcsm_na_output(mcsm_na_output_tsv):
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"""
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@param mcsm_na_na_outputcsv: file containing mcsm_na_na results for all muts
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which is the result of combining all mcsm_na_na batch results, and using
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@param mcsm_na_outputcsv: file containing mcsm_na_results for all muts
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which is the result of combining all mcsm_na batch results, and using
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bash scripts to combine all the batch results into one file.
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This is post run_get_results_mcsm_na_na.py
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Formatting df to a pandas df and output as tsv.
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This is post run_get_results_mcsm_na.py
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Formatting df to a pandas df and output as csv.
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@type string
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@return (not true) formatted mcsm_na_na output
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@return (not true) formatted csv for mcsm_na output
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@type pandas df
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"""
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@ -15,7 +15,7 @@ from format_results_mcsm_na import *
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# TODO: add cmd line args
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#gene = 'gid'
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gene = 'gid'
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drug = 'streptomycin'
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datadir = homedir + '/git/Data'
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indir = datadir + '/' + drug + '/input'
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@ -23,10 +23,10 @@ outdir = datadir + '/' + drug + '/output'
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outdir_na = outdir + '/mcsm_na_results/'
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# Input file
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infile_mcsm_na = outdir_na + 'gid_output_combined_clean.tsv'
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infile_mcsm_na = outdir_na + gene + '_output_combined_clean.tsv'
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# Formatted output file
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outfile_mcsm_na_f = outdir_na + 'gid_complex_mcsm_na_norm.csv'
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outfile_mcsm_na_f = outdir_na + gene + '_complex_mcsm_na_norm.csv'
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#==========================
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# CALL: format_results_mcsm_na()
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@ -45,4 +45,4 @@ print('Finished writing file:'
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, '\nExpected no. of cols:', len(mcsm_na_df_f.columns)
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, '\n=============================================================')
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#%%#####################################################################
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#%%#####################################################################
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