From 8fbf5bcaddc30d20395f609adae23493868625b0 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Thu, 12 Aug 2021 17:35:12 +0100 Subject: [PATCH] extracted results for dynamut gid bissection b10_21 --- dynamut/run_get_results_dynamut.py | 9 +++++++-- mcsm_na/format_results_mcsm_na.py | 10 +++++----- mcsm_na/run_format_results_mcsm_na.py | 8 ++++---- 3 files changed, 16 insertions(+), 11 deletions(-) diff --git a/dynamut/run_get_results_dynamut.py b/dynamut/run_get_results_dynamut.py index 423204a..2000fe3 100755 --- a/dynamut/run_get_results_dynamut.py +++ b/dynamut/run_get_results_dynamut.py @@ -31,8 +31,13 @@ outdir_dynamut_temp = outdir + 'dynamut_results/dynamut_temp/' #b09 and b10 failed, ran by Carlos, and returned results on 12 Aug # batch 9 and 10: RETRIEVED 12 Aug 09:25 -my_url_file = outdir_dynamut_temp + 'dynamut_result_url_gid_b10.txt' -my_suffix = 'gid_b10' +#my_url_file = outdir_dynamut_temp + 'dynamut_result_url_gid_b10.txt' +#my_suffix = 'gid_b10' + +# batch10_21: from bissection: humour me! (don't need since b10 ran +# from dynamut team, but still its ready to extract it!) +my_url_file = outdir_dynamut_temp + 'dynamut_result_url_gid_b10_21.txt' +my_suffix = 'gid_b10_21' #============================================================================== #========================== diff --git a/mcsm_na/format_results_mcsm_na.py b/mcsm_na/format_results_mcsm_na.py index 340dd15..7aa04da 100644 --- a/mcsm_na/format_results_mcsm_na.py +++ b/mcsm_na/format_results_mcsm_na.py @@ -21,14 +21,14 @@ from pandas.api.types import is_numeric_dtype def format_mcsm_na_output(mcsm_na_output_tsv): """ - @param mcsm_na_na_outputcsv: file containing mcsm_na_na results for all muts - which is the result of combining all mcsm_na_na batch results, and using + @param mcsm_na_outputcsv: file containing mcsm_na_results for all muts + which is the result of combining all mcsm_na batch results, and using bash scripts to combine all the batch results into one file. - This is post run_get_results_mcsm_na_na.py - Formatting df to a pandas df and output as tsv. + This is post run_get_results_mcsm_na.py + Formatting df to a pandas df and output as csv. @type string - @return (not true) formatted mcsm_na_na output + @return (not true) formatted csv for mcsm_na output @type pandas df """ diff --git a/mcsm_na/run_format_results_mcsm_na.py b/mcsm_na/run_format_results_mcsm_na.py index e738e90..cb7b4ca 100644 --- a/mcsm_na/run_format_results_mcsm_na.py +++ b/mcsm_na/run_format_results_mcsm_na.py @@ -15,7 +15,7 @@ from format_results_mcsm_na import * # TODO: add cmd line args -#gene = 'gid' +gene = 'gid' drug = 'streptomycin' datadir = homedir + '/git/Data' indir = datadir + '/' + drug + '/input' @@ -23,10 +23,10 @@ outdir = datadir + '/' + drug + '/output' outdir_na = outdir + '/mcsm_na_results/' # Input file -infile_mcsm_na = outdir_na + 'gid_output_combined_clean.tsv' +infile_mcsm_na = outdir_na + gene + '_output_combined_clean.tsv' # Formatted output file -outfile_mcsm_na_f = outdir_na + 'gid_complex_mcsm_na_norm.csv' +outfile_mcsm_na_f = outdir_na + gene + '_complex_mcsm_na_norm.csv' #========================== # CALL: format_results_mcsm_na() @@ -45,4 +45,4 @@ print('Finished writing file:' , '\nExpected no. of cols:', len(mcsm_na_df_f.columns) , '\n=============================================================') -#%%##################################################################### \ No newline at end of file +#%%#####################################################################