tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

extracted results for dynamut gid bissection b10_21

Browse source
This commit is contained in:
Tanushree Tunstall 2021-08-12 17:35:12 +01:00
parent 59a370b45a
commit 938dba7fcc
3 changed files with 16 additions and 11 deletions
Download patch file Download diff file Expand all files Collapse all files

9
dynamut/run_get_results_dynamut.py
View file

@ -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 #b09 and b10 failed, ran by Carlos, and returned results on 12 Aug
# batch 9 and 10: RETRIEVED 12 Aug 09:25 # batch 9 and 10: RETRIEVED 12 Aug 09:25
my_url_file = outdir_dynamut_temp + 'dynamut_result_url_gid_b10.txt' #my_url_file = outdir_dynamut_temp + 'dynamut_result_url_gid_b10.txt'
my_suffix = 'gid_b10' #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): def format_mcsm_na_output(mcsm_na_output_tsv):
""" """
@param mcsm_na_na_outputcsv: file containing mcsm_na_na results for all muts @param mcsm_na_outputcsv: file containing mcsm_na_results for all muts
which is the result of combining all mcsm_na_na batch results, and using which is the result of combining all mcsm_na batch results, and using
bash scripts to combine all the batch results into one file. bash scripts to combine all the batch results into one file.
This is post run_get_results_mcsm_na_na.py This is post run_get_results_mcsm_na.py
Formatting df to a pandas df and output as tsv. Formatting df to a pandas df and output as csv.
@type string @type string
@return (not true) formatted mcsm_na_na output @return (not true) formatted csv for mcsm_na output
@type pandas df @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 # TODO: add cmd line args
#gene = 'gid' gene = 'gid'
drug = 'streptomycin' drug = 'streptomycin'
datadir = homedir + '/git/Data' datadir = homedir + '/git/Data'
indir = datadir + '/' + drug + '/input' indir = datadir + '/' + drug + '/input'
@ -23,10 +23,10 @@ outdir = datadir + '/' + drug + '/output'
outdir_na = outdir + '/mcsm_na_results/' outdir_na = outdir + '/mcsm_na_results/'
# Input file # 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 # 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() # CALL: format_results_mcsm_na()