#!/usr/bin/python
# Copyright 2014 BARRIOT Roland
# This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    You should have received a copy of the GNU General Public License
#    along with this program.  If not, see <http://www.gnu.org/licenses/>.

import argparse
import time
import numpy as np
import h5py
from Prioritization import ScoreMatrix

# SCRIPT PARAMETERS
parser = argparse.ArgumentParser(description='ScoreMatrix initialization')
parser.add_argument('--file', required=True, help='ScoreMatrix file to create.')
parser.add_argument('--strain', required=True, help='Genome to fetch from CGDB.')
parser.add_argument('--datasource', default='unspecified', required=False, help='Datasource.')
parser.add_argument('--date', default=time.strftime('%Y-%m-%d'), required=False, help='Date of creation.')
parser.add_argument('--comment', default='no comment.', required=False, help='Some comments.')
parser.add_argument('--mode', default='alaR', required=False, help='Some comments.')
parser.add_argument('--ids', required=True, help='File containing identifiers.')
param = parser.parse_args()

info = {
	'strain': param.strain,
	'datasource': param.datasource,
	'date': param.date,
	'comment': param.comment,
	'mode': 'distance',
	'representation': 'alaR'
}

sm = ScoreMatrix()
sm.labels = {}

with open(param.ids) as f:
	content = f.read()
	lines = content.split('\n')

for i in xrange(len(lines)):
	sm.labels[lines[i]]=i

sm.matrix = np.empty( i*(i-1)/2,  dtype=np.float32)
sm.matrix[:] = np.NAN

sm.save(param.file, info)