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adde format_results_dynamut2.py and ran shiny scripts for barplots

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Tanushree Tunstall 2021-08-19 16:25:38 +01:00
parent 8cdf720702
commit f7aac58081
9 changed files with 235 additions and 59 deletions
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45
dynamut/run_format_results_dynamut.py
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@ -15,9 +15,9 @@ import os
homedir = os.path.expanduser('~')
os.chdir (homedir + '/git/LSHTM_analysis/dynamut')
from format_results_dynamut import *
from format_results_dynamut2 import *
########################################################################
# variables
# TODO: add cmd line args
gene = 'gid'
@ -26,28 +26,47 @@ datadir = homedir + '/git/Data'
indir = datadir + '/' + drug + '/input'
outdir = datadir + '/' + drug + '/output'
outdir_dynamut = outdir + '/dynamut_results/'
outdir_dynamut2 = outdir + '/dynamut_results/dynamut2/'
# Input file
infile_dynamut = outdir_dynamut + gene + '_dynamut_all_output_clean.csv'
infile_dynamut2 = outdir_dynamut2 + gene + '_dynamut2_output_combined_clean.csv'
# Formatted output filename
outfile_dynamut_f = outdir_dynamut + gene + '_complex_dynamut_norm.csv'
outfile_dynamut_f = outdir_dynamut2 + gene + '_complex_dynamut_norm.csv'
outfile_dynamut2_f = outdir_dynamut2 + gene + '_complex_dynamut2_norm.csv'
#==========================
# CALL: format_results_mcsm_na()
# Data: gid+streptomycin
#==========================
print('Formatting results for:', infile_dynamut)
dynamut_df_f = format_dynamut_output(dynamut_output_csv = infile_dynamut)
#===============================
# CALL: format_results_dynamut
# DYNAMUT results
# #===============================
# print('Formatting results for:', infile_dynamut)
# dynamut_df_f = format_dynamut_output(infile_dynamut)
# # writing file
# print('Writing formatted dynamut df to csv')
# dynamut_df_f.to_csv(outfile_dynamut_f, index = False)
# print('Finished writing file:'
# , '\nFile:', outfile_dynamut_f
# , '\nExpected no. of rows:', len(dynamut_df_f)
# , '\nExpected no. of cols:', len(dynamut_df_f.columns)
# , '\n=============================================================')
#===============================
# CALL: format_results_dynamut2
# DYNAMUT2 results
#===============================
print('Formatting results for:', infile_dynamut2)
dynamut2_df_f = format_dynamut2_output(infile_dynamut2) # dynamut2
# writing file
print('Writing formatted dynamut df to csv')
dynamut_df_f.to_csv(outfile_dynamut_f, index = False)
print('Writing formatted dynamut2 df to csv')
dynamut2_df_f.to_csv(outfile_dynamut2_f, index = False)
print('Finished writing file:'
, '\nFile:', outfile_dynamut_f
, '\nExpected no. of rows:', len(dynamut_df_f)
, '\nExpected no. of cols:', len(dynamut_df_f.columns)
, '\nFile:', outfile_dynamut2_f
, '\nExpected no. of rows:', len(dynamut2_df_f)
, '\nExpected no. of cols:', len(dynamut2_df_f.columns)
, '\n=============================================================')
#%%#####################################################################