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ran mcsm_na for rpob's RNAP complex i.e 5UHC

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Tanushree Tunstall 2021-11-19 07:48:42 +00:00
parent cee10cc540
commit 2925c89d11
7 changed files with 13 additions and 12 deletions
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0
mcsm_na/examples.py Normal file → Executable file
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mcsm_na/format_results_mcsm_na.py Normal file → Executable file
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mcsm_na/get_results_mcsm_na.py Normal file → Executable file
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mcsm_na/run_format_results_mcsm_na.py Normal file → Executable file
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@ -52,15 +52,16 @@ if not outdir:
outdir_na = outdir + 'mcsm_na_results/' outdir_na = outdir + 'mcsm_na_results/'
# Input file # Input file
infile_mcsm_na = outdir_na + gene + '_output_combined_clean.tsv' infile_mcsm_na = outdir_na + gene.lower() + '_output_combined_clean.tsv'
# Formatted output file # Formatted output file
outfile_mcsm_na_f = outdir_na + gene + '_complex_mcsm_na_norm.csv' outfile_mcsm_na_f = outdir_na + gene.lower() + '_complex_mcsm_na_norm.csv'
#========================== #===========================================
# CALL: format_results_mcsm_na() # CALL: format_results_mcsm_na()
# Data: gid+streptomycin # Data: gid+streptomycin
#========================== # Data: rpob+rifampicin, date: 18/11/2021
#===========================================
print('Formatting results for:', infile_mcsm_na) print('Formatting results for:', infile_mcsm_na)
mcsm_na_df_f = format_mcsm_na_output(mcsm_na_output_tsv = infile_mcsm_na) mcsm_na_df_f = format_mcsm_na_output(mcsm_na_output_tsv = infile_mcsm_na)

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mcsm_na/run_submit_mcsm_na.py
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@ -18,14 +18,14 @@ print(my_prediction_url)
# TODO: add cmd line args # TODO: add cmd line args
#gene = 'gid' #gene = 'gid'
drug = 'streptomycin' drug = ''
datadir = homedir + '/git/Data' datadir = homedir + '/git/Data/'
indir = datadir + '/' + drug + '/input' indir = datadir + drug + 'input/'
outdir = datadir + '/' + drug + '/output' outdir = datadir + drug + 'output/'
outdir_mcsm_na = outdir + 'mcsm_na_results' outdir_mcsm_na = outdir + 'mcsm_na_results/'
my_nuc_type = 'RNA' my_nuc_type = 'RNA'
my_pdb_file = indir + '/gid_complex.pdb' my_pdb_file = indir + gene.lower() + '_complex.pdb'
#============================================================================= #=============================================================================
# batch 26: 25.txt # RAN: 16 Feb: # batch 26: 25.txt # RAN: 16 Feb:

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mcsm_na/submit_mcsm_na.py Normal file → Executable file
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4
scripts/combining_dfs.py
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@ -122,8 +122,8 @@ if gene.lower() == "gid":
in_filename_mcsm = gene.lower() + '_complex_mcsm_norm_SRY.csv' # was incorrectly SAM previously in_filename_mcsm = gene.lower() + '_complex_mcsm_norm_SRY.csv' # was incorrectly SAM previously
if gene.lower() == "embb": if gene.lower() == "embb":
print("\nReading mCSM file for gene:", gene) print("\nReading mCSM file for gene:", gene)
#in_filename_mcsm = gene.lower() + '_complex_mcsm_norm1.csv' #in_filename_mcsm = gene.lower() + '_complex_mcsm_norm1.csv' #798
in_filename_mcsm = gene.lower() + '_complex_mcsm_norm2.csv' in_filename_mcsm = gene.lower() + '_complex_mcsm_norm2.csv' #844
if gene.lower() in gene_list_normal: if gene.lower() in gene_list_normal:
print("\nReading mCSM file for gene:", gene) print("\nReading mCSM file for gene:", gene)