conversions.py

#! /usr/bin/env python2
# -*- coding: utf-8 -*-


import argparse
import sys
import os
import pexpect
import subprocess
import pdb

#Other script imports
from hh_reader import read_result

#FUNCTIONS
def pdb_to_fasta(uid, outdir):
	'''Convert pdb file to fasta.
	'''

	inname = outdir+uid+'.pdb'
	outname = inname+'.fa'
	#Path to pdb parser
	command = 'python ./parse_pdb_resid.py ' + inname
	outp = subprocess.check_output(command, shell = True)#Save AA sequence
	outp = outp.decode()
	sequence = outp.split('\n')[0]
	with open(outname, "w") as outfile:
		outfile.write('>'+uid+'\n')
		i = 0 #index
		while i<len(sequence):
			outfile.write(sequence[i:i+60]+'\n')
			i+=60

	return None

def run_hhblits(uid, indir, hhblits, uniprot):
	'''A function that runs hhblits to create a HMM of an input sequence in fasta format
	'''


	inname = indir+uid+'.fa'
	outname = uid+'.hhm'
	statement = hhblits +' -i ' + inname + ' -d ' + uniprot + ' -ohhm ' + outname
	outp = subprocess.check_output(statement, shell = True)

	return None

def make_phylip(uids, query_aln, template_aln, outdir):
        '''Print phylip format for tree-puzzle calculations
        '''
        #Create text in phylip format
        text = (' 4  ' + str(len(query_aln)) + '\n'
                        + uids[0] + '00|' + query_aln + '\n'
                        + 'copy11111' + '|' + query_aln + '\n'
                        + uids[1] + '00|' + template_aln + '\n'
                        + 'copy22222' + '|' + template_aln + '\n')


        #Define file name
        file_name = uids[0] + '_' + uids[1] + '.phy'
        #Open file and write text to it
        with open(outdir+file_name, "w") as file:
                file.write(text)

        return None