added script to combined dfs of structural params like kd, dssp & rd

meta_data_analysis/combine_dfs.py

@@ -0,0 +1,152 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+'''
+Created on Tue Aug  6 12:56:03 2019
+
+@author: tanu
+'''
+#=============================================================================
+# Task: combine 3 dfs with aa position as linking column
+
+# Input: 3 dfs
+# pnca_dssp.csv
+# pnca_kd.csv
+# pnca_rd.csv
+
+# Output: .csv with 3)
+#=============================================================================
+#%% load packages
+import sys, os
+import pandas as pd
+#import numpy as np
+#=============================================================================
+#%% specify input and curr dir
+homedir = os.path.expanduser('~')
+
+# set working dir
+os.getcwd()
+os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis')
+os.getcwd()
+#=============================================================================
+#%% variable assignment: input and output 
+drug = 'pyrazinamide'
+gene = 'pncA'
+gene_match = gene + '_p.'
+
+#==========
+# data dir
+#==========
+#indir = 'git/Data/pyrazinamide/input/original'
+datadir = homedir + '/' + 'git/Data'
+
+#=======
+# input
+#=======
+#indir = 'git/Data/pyrazinamide/input/original'
+indir = datadir + '/' + drug + '/' + 'output'
+in_filename1 = 'pnca_dssp.csv'
+in_filename2 = 'pnca_kd.csv'
+in_filename3 = 'pnca_rd.csv'
+
+infile1 = indir + '/' + in_filename1
+infile2 = indir + '/' + in_filename2
+infile3 = indir + '/' + in_filename3
+
+print('\nInput path:', indir
+      , '\nInput filename1:', in_filename1
+      , '\nInput filename2:', in_filename2
+      , '\nInput filename3:', in_filename3
+      , '\n===================================================================')
+
+#=======
+# output 
+#=======
+outdir =   datadir + '/' + drug + '/' + 'output'
+out_filename = gene.lower() + '_struct_params.csv'
+outfile =  outdir + '/' + out_filename
+print('Output filename:', out_filename
+      , '\nOutput path:', outdir
+      , '\n===================================================================')
+
+#%% end of variable assignment for input and output files
+#=======================================================================
+#%%  Read input file
+dssp_df  = pd.read_csv(infile1, sep = ',')  
+kd_df  = pd.read_csv(infile2, sep = ',')  
+rd_df  = pd.read_csv(infile3, sep = ',')  
+
+print('Reading input files:'
+      , '\ndssp file:', infile1
+      , '\nNo. of rows:', len(dssp_df)
+      , '\nNo. of cols:', len(dssp_df.columns)
+      , '\nColumn names:', dssp_df.columns
+      , '\n==================================================================='
+      , '\nkd file:', infile2
+      , '\nNo. of rows:', len(kd_df)
+      , '\nNo. of cols:', len(kd_df.columns)
+      , '\nColumn names:', kd_df.columns
+      , '\n==================================================================='
+      , '\nrd file:', infile3
+      , '\nNo. of rows:', len(rd_df)
+      , '\nNo. of cols:', len(rd_df.columns)
+      , '\nColumn names:', rd_df.columns
+      , '\n===================================================================')
+
+#========================
+# checking no. of rows
+#========================
+print('Checking if no. of rows of the 3 dfs are equal:\n'
+      , len(dssp_df) == len(kd_df) == len(rd_df)
+      , '\nReason: fasta files and pdb files vary since not all pos are part of the structure'
+      , '\n===================================================================')
+
+#===================
+# concatenating dfs
+#===================
+
+expected_rows = max(len(dssp_df), len(kd_df), len(rd_df))
+
+# beware of harcoding! used for sanity check
+offset = 2 # 1 common col in each of the three dfs-1
+expected_cols = len(dssp_df.columns) + len(kd_df.columns) + len(rd_df.columns) - offset
+
+print('Combining dfs by commom col: position'
+      , '\nExpected nrows in combined_df:', expected_rows
+      , '\nExpected ncols in combined_df:', expected_cols
+      , '\nResetting the common col as the index'
+      , '\n===================================================================')
+
+dssp_df.set_index('position',inplace = True)
+kd_df.set_index('position',inplace = True)
+rd_df.set_index('position',inplace =True)
+
+combined_df = pd.concat([dssp_df, kd_df, rd_df], axis = 1, sort = False).reset_index()
+combined_df.rename(columns = {'index':'position'})
+
+print('Checking dimensions of concatenated df...')
+if len(combined_df) == expected_rows and len(combined_df.columns) == expected_cols:
+    print('PASS: combined df has expected dimensions'
+          , '\nNo. of rows in combined df:', len(combined_df)
+          , '\nNo. of cols in combined df:', len(combined_df.columns)
+          , '\n===============================================================')
+else:
+    print('FAIL: combined df has not expected dimensions'
+          , '\nNo. of rows in combined df:', len(combined_df)
+          , '\nNo. of cols in combined df:', len(combined_df.columns)
+          , '\n===============================================================')
+    
+#%% write file
+print('Writing file:'
+      , '\nFilename:', out_filename
+      , '\nPath:',  outdir
+      , '\n===================================================================')
+
+combined_df.to_csv(outfile, header = True, index = False)
+
+print('Finished writing:', out_filename
+      , '\nNo. of rows:', len(combined_df)
+      , '\nNo. of cols:', len(combined_df.columns)
+      , '\n===================================================================')
+
+#%% end of script
+#==============================================================================