#!/usr/bin/python

#filename: pdbminer.py

#####################################################################

# Search the protein sequence fasta file

# This code requires working biopython installed

# written by Bilal Nizami

#

# UKZN, Durban

# 2016

#

#

#####################################################################

#

# import functions

from __future__ import print_function

from optparse import OptionParser

from Bio import SeqIO

import sys

import re

from Bio.PDB import *

## Welcome message

print ('\n\tPDBMINER\n', 'written by Bilal Nizami\n', 'UKZN, Durban 2016\n\n\n', end="")

#==============================================================================

# Setting the options

#==============================================================================

parser = OptionParser("Usage: seqsearch.py -i --fasta fasta file name ")

parser.add_option("-i", "--fasta", type='string', dest="fasta",

help="A fasta file having amino acid sequence")

parser.add_option("-o", "--out", type='string', dest="output",

help="output text file")

parser.add_option("-p", "--path", type='string', dest="path",

help="string for path to the pdb files, it will be used for accesing the pdb file of parsed \

pdbid")

(options, args) = parser.parse_args()

#====================================================================

# if no arguments are passed

if options.fasta is None: # where fasta is obviously your required option

parser.print_help()

sys.exit(1)

#===========================================================================

#

# function to get the pdbid from fasta file

#===========================================================================

def fasta_get_pdbid(filename):

return pdbid;

#===========================================================================

# read the single fasta file containing the multiple sequences. #

pdb = []

fastafile = ''

seq = ''

aacid = []

A = R = N = D = B = C = E = Q = Z = G = H = I = L = K = M = F = P = S = T = W = Y = V = 0

#aminoacid = ['A', 'R', 'N', 'D', 'B', 'C', 'E', 'Q', 'Z', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V']

pdb_id = []

pdb_id_chain = []

pdbid = []

pdbchain = []

count = []

counter=0

sf = open(options.fasta, "rU")

pdbid = fasta_get_pdbid(options.fasta)

#print (pdbid)

#for pdb in pdbid:

for p in SeqIO.parse(sf, "fasta"): ## takes a file handle and format name, and returns a SeqRecord iterator using biopython SeqIO

#print (p.id)

#pdb_id_chain = re.findall("\d.{3}:[A-Z]", p.id)

#print (str(pdb_id_chain))

#pdb_id = re.findall("\d.{3}", str(pdb_id_chain))

#print (re.findall("\d.{3}", pdb_id[0]), end='')

#print ('PDBID"\t', pdb_id[0], end='')

#print ('PDBID and chain:\t', pdb_id_chain)

#pdbchain.append(pdb_id_chain)

#pdbid.append(pdb_id[0])

aacid = list(p.seq)

for aa in aacid:

if aa == 'A':

A=A+1

elif aa == 'R':

R=R+1

elif aa == 'N':

N=N+1

elif aa == 'D':

D=D+1

elif aa == 'B':

B=B+1

elif aa == 'C':

C=C+1

elif aa == 'E':

E=E+1

elif aa == 'Q':

Q=Q+1

elif aa == 'Z':

Z=Z+1

elif aa == 'G':

G=G+1

elif aa == 'H':

H=H+1

elif aa == 'I':

I=I+1

elif aa == 'L':

L=L+1

elif aa == 'K':

K=K+1

elif aa == 'M':

M=M+1

elif aa == 'F':

F=F+1

elif aa == 'P':

P=P+1

elif aa == 'S':

S=S+1

elif aa == 'T':

T=T+1

elif aa == 'W':

W=W+1

elif aa == 'V':

V=V+1

elif aa == 'Y':

Y=Y+1

counter=counter+1

#print ('. ', end="")

print ('total', counter, 'processed')

#print ('PDBID "\t', pdbid, pdbchain, end='')

sf.close()

#=============================================================================

# open Summary file and print into it

sf = open(options.output, 'w')

print('Amino Acid,', 'Count,', file=sf)

print('A\t', A, '\nR\t', R, '\nN\t', N, '\nD\t', D, '\nB\t', B, '\nC\t', C, '\nE\t', E, '\nQ\t', Q, '\nZ\t', Z, '\nG\t', G, '\nH\t', H, '\nI\t', I, '\nL\t', L, '\nK\t', K, '\nM\t', M, '\nF\t', F, '\nP\t', P, '\nS\t', S, '\nT\t', T, '\nW\t', W, '\nY\t', Y, '\nV\t', V, file=sf)

sf.close()

#===========================================================================================================

#

# sort and store only unique pdb ids, there might be redundent parsed pdbids due to seperate entry in input

# fasta file for multiple chains of a pdbid. it uses built in set() method

#

pdbid = list(set(pdbid)) # remove duplicates pdbids

#print (pdbid)

## opening file for dumping resolutions

sf = open('res.txt', 'w')

if options.path != None:

print ('Resolution', file=sf)

resolution = ''

pdb_path = []

parser = PDBParser()

for pdb in pdbid:

try:

pdb_dir = pdb[1:3]

pdb_dir = pdb_dir.lower()

pdb = pdb.lower() ## lower case, becuase last character fo pdbid from fasta file is in uppercase

#print (pdb)

pdb_path1 = str(options.path) + pdb_dir + '/pdb' + str(pdb) + '.ent' ## full path to the pdb.ent file

pdb_path.append(pdb_path1)

structure = parser.get_structure('PHA-L', pdb_path1)

resolution = str(structure.header['resolution'])

print ('for ', pdb)

print (resolution, file=sf)

#print (pdb_path)

except IOError:

print ('Can not find', pdb_path1, ' file')

#for pdb in pdb_path:

# try:

# #print (pdb)

# structure = parser.get_structure('PHA-L', pdb)

# resolution = str(structure.header['resolution'])

# print ('for ', pdb)

# print (resolution, file=sf)

# #print (resolution)

# except IOError:

# print ('Can not find', pdb ' file')

sf.close()