tidied and updated kd and dssp scripts & generated their respective outputs

meta_data_analysis/RD.py

@@ -5,28 +5,78 @@ Created on Thu Feb  6 12:18:24 2020
 
 @author: tanu
 """
-#http://foldxsuite.crg.eu/faq-page#
-# after fold x downlaoded, extract and run it from 
-#https://biopython.org/DIST/docs/api/Bio.PDB.ResidueDepth%27-module.html
-#proDepth: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007072
-#Depth server: http://cospi.iiserpune.ac.in/depth/htdocs/index.html
-# needs biopython and msms
+#=======================================================================
+# Task: Residue Depth (rd) values for amino acid sequence using the
+# Depth server.
+# Depth server: http://cospi.iiserpune.ac.in/depth/htdocs/index.html
+# FIXME: for now input is a valid pdb code NOT a valid pdb file that you can upload
+# Input: PDB file  (valid pdb code)
 
-# load libraries 
+# Output: 
+
+# useful links
+# http://foldxsuite.crg.eu/faq-page#
+# after fold x downlaoded, extract and run it from 
+# https://biopython.org/DIST/docs/api/Bio.PDB.ResidueDepth%27-module.html
+# proDepth: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007072
+# needs biopython and msms
+#=======================================================================
+#%% load packages
 import sys, os
+import re
 import pandas as pd
 from Bio.PDB.ResidueDepth import ResidueDepth
 from Bio.PDB.PDBParser import PDBParser
 from Bio.PDB.ResidueDepth import get_surface
 
-#%%
+#%% specify input and output variables
 homedir = os.path.expanduser('~') # spyder/python doesn't recognise tilde
+
+# set working dir
 os.getcwd()
-os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis/struct_params')
+os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis')
 os.getcwd()
-#%%
+#=======================================================================
+#%% variable assignment: input and output paths & filenames
+drug = 'pyrazinamide'
+gene = 'pncA'
+gene_match = gene + '_p.'
+
+#==========
+# data dir
+#==========
+#indir = 'git/Data/pyrazinamide/input/original'
+datadir = homedir + '/' + 'git/Data'
+
+#=======
+# input
+#=======
+indir = datadir + '/' + drug + '/' + 'input'
+in_filename = '3pl1.pdb'
+infile = indir + '/' + in_filename
+print('Input filename:', in_filename
+      , '\nInput path:', indir)
+
+#=======
+# output 
+#=======
+outdir = datadir + '/' + drug + '/' + 'output'
+# specify output file 
+out_filename = 'XXX'
+outfile =  outdir + '/' + out_filename
+print('Output filename: ', out_filename
+      , '\nOutput path: ', outdir)
+
+#%% end of variable assignment for input and output files
+#================================================================
+# Read input pdb file
 parser = PDBParser()
-structure = parser.get_structure("3pl1", "/home/tanu/git/3pl1.pdb")
+
+# extract the 3 letter pdb code
+pdb_code = re.search(r'(^[0-9]{1}\w{3})', in_filename).group(1)
+
+#structure = parser.get_structure("3pl1", "/home/tanu/git/3pl1.pdb")
+structure = parser.get_structure(pdb_code, infile)
 model = structure[0]
 surface = get_surface(model)
 
@@ -38,7 +88,7 @@ rd.property_keys
 baz = rd.property_list
 
 
-#To calculate the residue depth (average atom depth of the atoms in a residue):
+# To calculate the residue depth (average atom depth of the atoms in a residue):
 from Bio.PDB.ResidueDepth import residue_depth
 chain = model['A']
 res152 = chain[152]