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extracted results for dynamut gid bissection b10_21

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Tanushree Tunstall 2021-08-12 17:35:12 +01:00
parent 59a370b45a
commit 938dba7fcc
3 changed files with 16 additions and 11 deletions
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9
dynamut/run_get_results_dynamut.py
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@ -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'
#==============================================================================
#==========================

10
mcsm_na/format_results_mcsm_na.py
View file

@ -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
"""

6
mcsm_na/run_format_results_mcsm_na.py
View file

@ -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()