tidied and updated kd and dssp scripts & generated their respective outputs
This commit is contained in:
parent
87a847109a
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6 changed files with 209 additions and 181 deletions
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@ -5,28 +5,78 @@ Created on Thu Feb 6 12:18:24 2020
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@author: tanu
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"""
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#http://foldxsuite.crg.eu/faq-page#
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# after fold x downlaoded, extract and run it from
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#https://biopython.org/DIST/docs/api/Bio.PDB.ResidueDepth%27-module.html
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#proDepth: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007072
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#Depth server: http://cospi.iiserpune.ac.in/depth/htdocs/index.html
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# needs biopython and msms
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#=======================================================================
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# Task: Residue Depth (rd) values for amino acid sequence using the
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# Depth server.
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# Depth server: http://cospi.iiserpune.ac.in/depth/htdocs/index.html
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# FIXME: for now input is a valid pdb code NOT a valid pdb file that you can upload
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# Input: PDB file (valid pdb code)
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# load libraries
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# Output:
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# useful links
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# http://foldxsuite.crg.eu/faq-page#
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# after fold x downlaoded, extract and run it from
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# https://biopython.org/DIST/docs/api/Bio.PDB.ResidueDepth%27-module.html
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# proDepth: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007072
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# needs biopython and msms
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#=======================================================================
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#%% load packages
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import sys, os
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import re
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import pandas as pd
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from Bio.PDB.ResidueDepth import ResidueDepth
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from Bio.PDB.PDBParser import PDBParser
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from Bio.PDB.ResidueDepth import get_surface
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#%%
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#%% specify input and output variables
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homedir = os.path.expanduser('~') # spyder/python doesn't recognise tilde
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# set working dir
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os.getcwd()
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os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis/struct_params')
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os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis')
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os.getcwd()
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#%%
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#=======================================================================
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#%% variable assignment: input and output paths & filenames
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drug = 'pyrazinamide'
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gene = 'pncA'
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gene_match = gene + '_p.'
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#==========
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# data dir
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#==========
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#indir = 'git/Data/pyrazinamide/input/original'
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datadir = homedir + '/' + 'git/Data'
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#=======
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# input
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#=======
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indir = datadir + '/' + drug + '/' + 'input'
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in_filename = '3pl1.pdb'
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infile = indir + '/' + in_filename
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print('Input filename:', in_filename
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, '\nInput path:', indir)
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#=======
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# output
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#=======
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outdir = datadir + '/' + drug + '/' + 'output'
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# specify output file
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out_filename = 'XXX'
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outfile = outdir + '/' + out_filename
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print('Output filename: ', out_filename
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, '\nOutput path: ', outdir)
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#%% end of variable assignment for input and output files
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#================================================================
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# Read input pdb file
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parser = PDBParser()
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structure = parser.get_structure("3pl1", "/home/tanu/git/3pl1.pdb")
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# extract the 3 letter pdb code
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pdb_code = re.search(r'(^[0-9]{1}\w{3})', in_filename).group(1)
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#structure = parser.get_structure("3pl1", "/home/tanu/git/3pl1.pdb")
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structure = parser.get_structure(pdb_code, infile)
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model = structure[0]
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surface = get_surface(model)
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@ -38,7 +88,7 @@ rd.property_keys
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baz = rd.property_list
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#To calculate the residue depth (average atom depth of the atoms in a residue):
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# To calculate the residue depth (average atom depth of the atoms in a residue):
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from Bio.PDB.ResidueDepth import residue_depth
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chain = model['A']
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res152 = chain[152]
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@ -1,68 +1,85 @@
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#!/home/tanu/anaconda3/envs/ContactMap/bin/python3
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# Read a DSSP file into a data frame and pretty-print it
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#https://jbloomlab.github.io/dms_tools2/dms_tools2.dssp.html
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#https://jbloomlab.github.io/dms_tools2/dms_tools2.dssp.html
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import sys, os
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import re
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import pandas as pd
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from Bio.PDB import PDBParser
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from Bio.PDB.DSSP import DSSP
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import pandas as pd
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import pprint as pp
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#from Bio.PDB.PDBParser import PDBParser
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import dms_tools2
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import dms_tools2.dssp
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#%%
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# my working dir
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homedir = os.path.expanduser('~') # spyder/python doesn't recognise tilde
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os.getcwd()
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os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis/struct_params')
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os.getcwd()
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#%%
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# sample example
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dssp_file = "./3pl1.dssp"
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dssp_df = dms_tools2.dssp.processDSSP(dssp_file, chain='A')
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#%% specify input and output variables
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homedir = os.path.expanduser('~')
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# outputs to console
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#returns df with ASA and RSA (base on Tien at al 2013 (theor.) values)
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#Link: https://en.wikipedia.org/wiki/Relative_accessible_surface_area
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#%% set working dir
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os.getcwd()
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os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis')
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os.getcwd()
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#=======================================================================
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#%% variable assignment: input and output paths & filenames
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drug = 'pyrazinamide'
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gene = 'pncA'
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#gene_match = gene + '_p.'
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#==========
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# data dir
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#==========
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#indir = 'git/Data/pyrazinamide/input/original'
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datadir = homedir + '/' + 'git/Data'
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#=======
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# input
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#=======
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indir = datadir + '/' + drug + '/' + 'output'
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#in_filename = 'pnca.dssp'
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in_filename = gene.lower() +'.dssp'
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infile = indir + '/' + in_filename
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print('Input filename:', in_filename
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, '\nInput path:', indir)
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# specify PDB chain
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my_chain = 'A'
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#=======
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# output
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#=======
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outdir = datadir + '/' + drug + '/' + 'output'
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out_filename = gene.lower() + '_dssp_df'
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outfile = outdir + '/' + out_filename
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print('Output filename:', out_filename
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, '\nOutput path:', outdir
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,'\nOutfile: ', outfile)
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#%% end of variable assignment for input and output files
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#================================================================
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# Process dssp output and extract into df
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dssp_file = infile
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dssp_df = dms_tools2.dssp.processDSSP(dssp_file, chain = my_chain)
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# returns df with ASA and RSA (base on Tien at al 2013 (theor.) values)
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# Link: https://en.wikipedia.org/wiki/Relative_accessible_surface_area
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pp.pprint(dssp_df)
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# write to csv
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dssp_df.to_csv('3pl1_dssp_df', header=True, index = False)
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# Rename column (amino acid) as 'wild_type' and (site} as 'position'
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# to be the same names as used in the file required for merging later.
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dssp_df.columns
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dssp_df.rename(columns = {'site':'position', 'amino_acid':'wild_type'}, inplace = True)
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dssp_df.columns
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#%% specify variables for input and output paths and filenames
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drug = "pyrazinamide"
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#gene = "pnca"
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#%% Write ouput csv file
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print('Writing file:', outfile
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, '\nFilename:', out_filename
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, '\nPath:', outdir)
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datadir = homedir + "/git/Data"
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basedir = datadir + "/" + drug + "/input"
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# input
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inpath = "/processed"
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in_filename = "/3pl1.dssp"
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infile = basedir + inpath + in_filename
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#print(infile)
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# output file
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outpath = "/output"
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outdir = datadir + "/" + drug + outpath
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out_filename = "/3pl1_dssp_df"
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outfile = outdir + out_filename
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print(outdir); print(outfile)
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if not os.path.exists(datadir):
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print('Error!', datadir, 'does not exist. Please ensure it exists. Dir struc specified in README.md')
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os.makedirs(datadir)
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exit()
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if not os.path.exists(outdir):
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print('Error!', outdir, 'does not exist.Please ensure it exists. Dir struc specified in README.md')
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exit()
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else:
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print('Dir exists: Carrying on')
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# end of variable assignment for input and output files
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#%% <----- fixme
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dssp_file = infile
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dssp_df = dms_tools2.dssp.processDSSP(dssp_file, chain='A')
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#%%
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# write to csv
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dssp_df.to_csv(outfile, header=True, index = False)
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print('Finished writing:', out_filename
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, '\nNo. of rows:', len(dssp_df)
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, '\nNo. of cols:', len(dssp_df.columns))
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print('======================================================================')
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@ -5,3 +5,32 @@
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# - Create eg: '~/git/Data/{original,processed}
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# - Create eg: '~/git/Data/processed/' + drug (for each drug)
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# - Create eg: '~/git/Data/output/' + drug + '{plots, structure}'
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#%% specify homedir as python doesn't recognise tilde
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homedir = os.path.expanduser('~')
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#%% variable assignment: input and output paths & filenames
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drug = 'pyrazinamide'
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gene = 'pncA'
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gene_match = gene + '_p.'
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#==========
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# data dir
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#==========
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#indir = 'git/Data/pyrazinamide/input/original'
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datadir = homedir + '/' + 'git/Data'
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#==========
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# input dir
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#==========
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indir = datadir + '/' + drug + '/' + 'input'
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#============
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# output dir
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#============
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# several output files
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outdir = datadir + '/' + drug + '/' + 'output'
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#%%end of variable assignment for input and output files
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#==============================================================================
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@ -6,7 +6,8 @@ Created on Tue Aug 6 12:56:03 2019
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@author: tanu
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'''
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#=======================================================================
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# Task: Hydrophobicity (Kd) values for amino acid sequence using the Kyt&-Doolittle
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# Task: Hydrophobicity (Kd) values for amino acid sequence using the
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# Kyt&-Doolittle.
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# Same output as using the expasy server https://web.expasy.org/protscale/
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# useful links
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@ -102,7 +103,7 @@ print('======================================================================')
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# which will allow easy merging of the two dfs.
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# df1: df of aa seq with index reset to start from 1 (reflective of the actual aa position in a sequence)
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# col name for wt is the same as reflected in the the AF_OR file to allow easy merging
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# Name column of wt as 'wild_type' to be the same name used in the file required for merging later.
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dfSeq = pd.DataFrame({'wild_type':list(sequence)})
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dfSeq.index = np.arange(1, len(dfSeq) + 1) # python is not inclusive
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@ -1,72 +0,0 @@
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#!/usr/bin/python
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# Read a PDB and output DSSP to console
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import sys, os
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from Bio.PDB import PDBParser
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from Bio.PDB.DSSP import DSSP
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import pandas as pd
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import pprint as pp
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#%%
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# TASK: read a pdb file and generate a dssp output file
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# FIXME: Pending output dssp hasn't been generated
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# needs dssp exe on linux
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# may be easier to run the dssp exe locally
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#%%
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# my working dir
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os.getcwd()
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homedir = os.path.expanduser('~') # spyder/python doesn't recognise tilde
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os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis')
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os.getcwd()
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#%%
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# specify variables for input and output paths and filenames
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drug = "pyrazinamide"
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#gene = "pnca"
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datadir = homedir + "/git/Data"
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basedir = datadir + "/" + drug + "/input"
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# input
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inpath = "/original"
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# uncomment as necessary
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in_filename = "/3pl1.pdb"
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infile = basedir + inpath + in_filename
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#print(infile)
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# output file
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outpath = "/processed"
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outdir = datadir + "/" + drug + outpath
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out_filename = "/3pl1.dssp"
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outfile = outdir + out_filename
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#print(outdir)
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if not os.path.exists(datadir):
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print('Error!', datadir, 'does not exist. Please ensure it exists. Dir struc specified in README.md')
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os.makedirs(datadir)
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exit()
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if not os.path.exists(outdir):
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print('Error!', outdir, 'does not exist.Please ensure it exists. Dir struc specified in README.md')
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exit()
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else:
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print('Dir exists: Carrying on')
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# end of variable assignment for input and output files
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#%%
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p = PDBParser()
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structure = p.get_structure("3pl1", infile)
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model = structure[0]
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dssp = DSSP(model, infile)
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#dssp = DSSP(model, infile, dssp='mkdssp') #incase you used DSSP2 exe
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pp.pprint(dssp)
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#DSSP data is accessed by a tuple - (chain id, residue id): RSA
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a_key = list(dssp.keys())[3]
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dssp[a_key]
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pp.pprint(dssp.keys())
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pp.pprint(dssp.property_dict)
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pp.pprint(dssp.property_keys)
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pp.pprint(dssp.property_list)
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#!/usr/bin/env python3
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# -*- coding: utf-8 -*-
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"""
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Created on Sun Feb 16 11:21:44 2020
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#!/bin/bash
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#=======================================================================
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# Task: read a pdb file and generate a dssp output file
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# Input:
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# pdb file
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@author: tanu
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"""
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#!/usr/bin/bash
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# Run dssp exe
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# Output:
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# pdb_code.dssp
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# needs dssp exe on linux
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# more efficient to run dssp exe locally
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#%%
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# specify variables for input and output paths and filenames
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drug="pyrazinamide"
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#gene = "pnca"
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# note: double quotes for variable interpolation
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#=======================================================================
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# #%%specify variables for input and output paths and filenames
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drug='pyrazinamide'
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gene='pncA'
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#convert to lowercase for consistency in filenames
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gene_l=$(printf $gene | awk '{print tolower($0)}')
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gene_match="${gene}_p."
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#printf "${gene_match}\n"
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datadir="~git/Data"
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basedir=${datadir}"/"${drug}
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echo${basedir}
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#==========
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# data dir
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#==========
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#indir = 'git/Data/pyrazinamide/input/original'
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#datadir="~git/Data"
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datadir="${HOME}/git/Data"
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#=======
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# input
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inpath="/original"
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#=======
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indir=${datadir}'/'${drug}'/input'
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printf "Input dir: ${indir}\n"
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in_filename='3pl1.pdb'
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#infile=${basedir}${inpath}${in_filename}
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infile=${indir}'/'${in_filename}
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printf "Input file: ${infile}\n"
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# uncomment as necessary
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in_filename="/3pl1.pdb"
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#=======
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# output
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#=======
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outdir=${datadir}'/'${drug}$'/output'
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printf "Output dir: ${outdir}"
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#out_filename='3pl1.dssp'
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out_filename="${gene_l}.dssp"
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outfile=${outdir}'/'${out_filename}
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printf "Output file: ${outfile}\n"
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infile=${basedir}${inpath}${in_filename}
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echo${infile}
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# output file
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outpath="/processed"
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outdir=${datadir}"/"${drug}${outpath}
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out_filename="/3pl1.dssp"
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outfile=${outdir}${out_filename}
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echo${outdir}
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if not os.path.exists(datadir):
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print('Error!', datadir, 'does not exist. Please ensure it exists. Dir struc specified in README.md')
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os.makedirs(datadir)
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exit()
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if not os.path.exists(outdir):
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print('Error!', outdir, 'does not exist.Please ensure it exists. Dir struc specified in README.md')
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exit()
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else:
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print('Dir exists: Carrying on')
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# end of variable assignment for input and output files
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#%%
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# ommand line args
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dssp -i 3pl1.pdb -o 3pl1.dssp
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dssp -i
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#%%end of variable assignment for input and output files
|
||||
#================================================================
|
||||
# command line arg to run dssp and create output file
|
||||
dssp -i ${infile} -o ${outfile}
|
||||
printf "Finished writing: ${outfile}\n"
|
||||
#printf "Filename: ${out_filename}\nlocated in: ${outdir}\n"
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue