tanu/LSHTM_analysis
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Tanushree Tunstall 2021-02-10 11:53:20 +00:00
parent 600f829972
commit 0fd3e75ab0
4 changed files with 6 additions and 6 deletions
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0
dynamut/dynamut_test.py → dynamut/get_results.py
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0
dynamut/dynamut_reading_muts.py → dynamut/reading_muts.py
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10
mcsm/run_mcsm.py
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@ -26,14 +26,14 @@ arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb fi
arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
# stage: submit, output url file
arg_parser.add_argument('--url_file', help = 'Output results url file. The result of stage "submit". By default, it creates a output result url file in the output dir: "output_dir + gene.lower() + _result_urls.txt")
arg_parser.add_argument('--url_file', help = 'Output results url file. The result of stage "submit". By default, it creates a output result url file in the output dir: "output_dir + gene.lower() + _result_urls.txt" ')
# stage: get, intermediate mcsm output file
arg_parser.add_argument('--outfile_scraped', help = 'Output mcsm results scraped. The result of stage "get". By default, it creates an interim output file in the output dir: "output_dir + gene.lower() +_mcsm_output.csv")
arg_parser.add_argument('--outfile_scraped', help = 'Output mcsm results scraped. The result of stage "get". By default, it creates an interim output file in the output dir: "output_dir + gene.lower() +_mcsm_output.csv" ')
# stage: format, formatted output with scaled values, etc
# FIXME: Don't call this stage until you have ALL the interim results for your snps as the normalisation will be affected!
arg_parser.add_argument('--outfile_formatted', help = 'Output mcsm results formatted. The result of stage "format". By default, it creates a formatted output file in the output dir: "output_dir + gene.lower() + _complex_mcsm_norm.csv")
arg_parser.add_argument('--outfile_formatted', help = 'Output mcsm results formatted. The result of stage "format". By default, it creates a formatted output file in the output dir: "output_dir + gene.lower() + _complex_mcsm_norm.csv" ')
arg_parser.add_argument('--debug', action='store_true', help = 'Debug Mode')
@ -103,7 +103,7 @@ infile_pdb = indir + '/' + in_filename_pdb
if mutation_filename:
in_filename_snps = mutation_filename
else:
in_filename_snps = gene.lower() + '_mcsm_snps.csv'
in_filename_snps = gene.lower() + '_mcsm_formatted_snps.csv'
infile_snps = outdir + '/' + in_filename_snps
@ -111,7 +111,7 @@ infile_snps = outdir + '/' + in_filename_snps
# output
#=======
# mcsm_results globals
if not result_url:
if not result_urls:
result_urls_filename = gene.lower() + '_result_urls.txt'
result_urls = outdir + '/' + result_urls_filename
if DEBUG:

2
scripts/my_pdbtools/pdbtools

@ -1 +1 @@
Subproject commit 881ff8f27aaf1db4266a84fb03baad3dab552c64
Subproject commit eadbb223f3883be8730ba39e751a24f5ce0cd45d