dmp2rr.py

#!/usr/bin/python

################################################################################################################################
# this program generates distance-based input (rr) file from distance map histogram (rawdistpred.current) generated by DMPfold #
################################################################################################################################

import operator
import os
import math
import sys
import optparse    # for option sorting
import random
from decimal import *
getcontext().prec = 4
parser = optparse.OptionParser()
parser.add_option('-d', dest='dist',
        default = '',    # default empty
        help = 'name of raw distance map (DMPfold distogram)')
parser.add_option('-a', dest='fasta',
        default = '',    # default empty
        help = 'name of fasta file')


parser.add_option('-r', dest='rr',
        default = 'out',    # default out
        help = 'name of output contact map')

(options,args) = parser.parse_args()
dist = options.dist
fasta = options.fasta
rr = options.rr
try:
        ffasta = open(fasta, 'r')
        flines = ffasta.readlines()
except IOError:
        sys.exit()
        print ('skipping..')

frr = open(rr, 'w')
frr.write(flines[1].strip())
frr.write('\n')



try:
        f = open(dist, 'r')
        lines = f.readlines()
        rrList = []
        for line in lines:
                line = line.split()

                try:
                        res1 = int(line[0])
                        res2 = int(line[1])
                except ValueError:
                        print ('value error..')
                        continue

                count = 0
                for i in range(2, 14):
                        th = i
                        count += (float(line[i])) #Decimal(float(line[i]))
                        if (count >= 0.85):

                                break


                if (th <= 9):
                        th = 8
                elif (th > 9 and th <= 11):
                        th = 10
                elif (th > 11 and th <= 13):
                        th = 12
                if (count < 0.0001):
                        count = 0.0001
                rrList.append([str(res1), str(res2), str(th), str(count)])
        f.close()
        dict1 = {}
        for x in rrList:
                dict1[(x[0], x[1], x[2])] = x[3]
        sorted_rr = sorted(dict1.items(), key=operator.itemgetter(1))
        sorted_rr.reverse()
        count = 0
        for sr in sorted_rr:
                (i, j, th), p = sr[0], sr[1]

                frr.write(str(i))
                frr.write(' ')
                frr.write(str(j))
                frr.write(' ')
                frr.write('0')
                frr.write(' ')
                frr.write(th)
                frr.write(' ')
                frr.write(str(p))
                frr.write('\n')
                count += 1
except IOError:

        print ('skippig..')


ffasta.close()
frr.close()