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refactor foldx pipeline to include:

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* command-line args
* creating necessary dirs automagically
* code cleanup, syntax errors, etc etc
This commit is contained in:
Tanushree Tunstall 2020-06-30 17:14:30 +01:00
parent e8a66a7a94
commit 973a1a33da
12 changed files with 700 additions and 56 deletions
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12
scripts/combine_afs_ors.py
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@ -71,7 +71,7 @@ infile2 = outdir + '/' + in_filename_afor_kin
print('Input file0:', infile0
, '\nInput file1:', infile1
, '\nInput file2:', infile2
, '\n===================================================================')
, '\n=============================================================')
#=======
# output
@ -79,7 +79,7 @@ print('Input file0:', infile0
out_filename = gene.lower() + '_metadata_afs_ors.csv'
outfile = outdir + '/' + out_filename
print('Output file:', outfile
, '\n===================================================================')
, '\n=============================================================')
del(in_filename_afor, in_filename_afor_kin, datadir, indir, outdir)
@ -217,13 +217,7 @@ if fail:
del(left_df, right_df, common_cols, merging_cols, nmerging_cols, my_join, ndiff1, ndiff2, missing_mutinfo
, expected_rows, expected_cols, fail)
del(afor_df, snpinfo_df)
#=======================================================================
#%% Second merge: combined_df1 and afor_kin_df