#!/usr/bin/env python
# _*_coding:utf-8_*_

import sys, os, re

pPath = re.sub(r'scripts$', '', os.path.split(os.path.realpath(__file__))[0])
sys.path.append(pPath)
from pubscripts import read_fasta_sequences
import argparse

dbName = '/home/zchen/Databases/uniref50/uniref50'
ncbidir = '/home/zchen/local/Tools/blast-2.2.18/bin'


def generatePSSMProfile(fastas, outDir, blastpgp, db):
    """
    Generate PSSM file by using the blastpgp program in NCBI blast-2.2.18 package.

    Parameters
    ----------
    file : file
        the file, which include the protein sequences in fasta format.

    blastpgp: string
        the path of blastpgp program.

    db: string
        the uniref50 data base, which is formated by the 'formatdb' program in blast package.

    Returns
    -------
    a string:
        A directory name, which include the predicted protein PSSM information.
    """

    if os.path.exists(outDir) == False:
        os.mkdir(outDir)

    for i in fastas:
        name, sequence = re.sub('\|', '', i[0]), i[1]
        with open(name + '.txt', 'w') as f:
            f.write('>' + name + '\n' + sequence + '\n')
        myCmd = blastpgp + ' -i ' + name + '.txt' + ' -d ' + db + ' -b 0 -v 5000 -j 3 -h 0.001 -Q ' + outDir + '/' + name + '.pssm'
        print('Doing psiblast for protein: ' + name)
        os.system(myCmd)
        os.remove(name + '.txt')
    return outDir


if __name__ == '__main__':
    parser = argparse.ArgumentParser(usage="it's usage tip.", description="generate PSSM profile")
    parser.add_argument("--file", required=True, help="protein sequence file in fasta format")
    parser.add_argument("--blastpgp", help="the path of NCBI psiblast program")
    parser.add_argument("--db", help="the path of unief50 database")
    args = parser.parse_args()

    blastpgp = args.blastpgp if args.blastpgp != None else ncbidir + '/blastpgp'
    db = args.db if args.db != None else dbName
    fastas = read_fasta_sequences.readFasta(args.file)
    outputDir = generatePSSMProfile(fastas, 'out', blastpgp, db)
    print('The PSSM profiles are stored in directory: ' + outputDir)








